The Contingency
by Deliwiel
Summary: What if Thornton is innocent, and she is not actually Chrysalis? How will the team find out, and will they found out in time to save her before something terrible happens to the person they used to call a boss, a friend? Rated T for wounds and for my paranoia's sake
1. Chapter 1

_**If I'm posting this, it means that the season did NOT end the way I thought it should have, Thornton-wise anyway, so I wrote this contingency story of how I thought things should have turned out. Or heck. Maybe things did turn out OK and I just wanted to post this anyways... guess that means you gotta go watch the episode! ;) XD**_

 _ **Yes, I know, Nikki is a part of this story *hiss* I kinda didn't like myself cuz I had to add her in. You couldn't really go anywhere with Thornton and not have Nikki, but we've seen Nikki all of three times I think? So if she's OOC, it's because of that ;)**_

 _ **Also, this first chapter is pretty long, but I'm not gonna promise that the other chapters are gonna be as long. In fact, I can almost promise that they won't be XD**_

 _ **Okay, I know that Jack hasn't actually told us what happened between him and Matty, but for this story, we're going to pretend like he did...**_

Jack walked into the war room, searching for his friend. He spotted the blond, but was slightly concerned when he saw the look on the kid's face. "Hey," Jack said, sitting down next to the troubled-looking MacGyver. "What's eatin' ya?"

"Nothing, I'm fine," Mac brushed off his friend's concern, not sure if he wanted to voice his thoughts out loud yet.

"Remember how you wouldn't stop bugging me about what happened between Matty and me?" Jack asked, poking his friend in the arm. "That's gonna be me this time," he informed the blond. "I'm just gonna keep bugging you till you tell me what's goin' on in that big brain of yours. And you've heard me, I can go on for hours and hours and hours. I could serenade you, I could quote all of the Die Hard movies, or any Bruce Willis movie for that matter, and it ain't gonna stop until you tell me what you're thinkin' about," Jack insisted. Mac raised his eyebrow at his older partner, almost in a challenging manner. Jack got an evil glint in his eyes.

 _"To all the girls I've loved before," Jack began with a smirk. "Who travelled in and out my door; I'm glad they came along! I dedicate this song to all the girls I've loved before-"_

"Really?" MacGyver said with a laugh. "All the popular Willie Nelson songs you could have chosen from, and you choose that one?"

"Hey, he and Julio Iglesias made the song work, man," Jack insisted. "Such different voices, but when you put them together, it just...worked. Can I keep going?" Jack asked.

"No, no," Mac said, pretending to beg. At least, mostly pretending. "Alright. I'll tell you what's bugging me," he caved. "Because that's what family does; we tell each other what's wrong, and we don't take months after we meet our new boss to do so," he added, elbowing his friends in the ribs.

"Aiyee," Jack said, shying away from his friend's knobby elbow. "I finally told you, didn't I?" he asked incredulously.

"Took you long enough to do it though," Mac reminded him.

"Eh, debatable. Anyway, tell me what's wrong," Jack said, turning to face his friend more fully on the couch.

"I've got a date with Nikki tonight," Mac admitted.

"Wait...so I chose the right song to serenade you with!" Jack exclaimed with a laugh. "But that's not a face that says you're happy about your plans with her," he pointed out, referring to the expression that had taken residence on MacGyver's face.

"It's just… I dunno Jack. Something's just felt...wrong ever since she came back, I guess," he finally said.

"Well, it's probably because you're having conflicted feelings," Jack said. "You were so relieved to get Nikki back, but the cost of her coming back was finding out Thornton, the boss who seemed like she always watched our backs and was always there for us, was a mole. That'd make me have mixed feelings about my old girlfriend for a little while too, but seriously Mac. It's been months, and you've seen Nikki all of two times since she got back, at least to my knowledge," Jack said. "You've gotta face the feelings sometime, brother."

"It's not that," Mac said. "Or at least, not completely. Call it a gut feeling Jack, but something just isn't sitting right with me about this whole 'mole' situation. I think I've pushed it aside because I was just happy Nikki turned out not to be a traitor. I was willing to overlook things, but the more I look at it, the less comfortable I feel with everything. I also got a call from the prison," Mac added. "They told me that Thornton wants to talk with me as soon as I can."

"Why?" Jack asked, scrunching his face up in confusion.

"How am I supposed to know?" Mac asked, rolling his eyes at his partner. "My guess is that's what I'm supposed to find out when I go talk to her," he added sarcastically.

"Wait, you're not actually gonna do it, are you?"

"I think I will," Mac replied. "I mean, what can she do to me? We'll be in a secure facility, with guards around us. I don't think I'll be in danger," he pointed out.

"When are you gonna go?"

"I was thinking Monday."

"Any particular reason for the wait?"

"Well, there's the thing with Nikki tonight, and then I want to have the weekend to make sure my head is clear and I'm thinking things through logically," Mac replied.

"Fair enough," Jack said. He could still tell his friend looked troubled though, so he continued talking. "Listen," Jack said, putting a hand on Mac's shoulder. "Go see your girl tonight. I'm sure your conflicted feelings are all just a form of survivor's guilt," he tried.

"You...you do know what survivor's guilt is, right?" Mac asked, staring at his friend while raising one eyebrow.

"Yes I know what survivor's guilt is," Jack replied drily. "Like I said-a _form_ of survivor's guilt."

"Whatever, man," Mac relented with a chuckle.

"But you're gonna go see Nikki tonight?" Jack asked, staring at his partner intently. Mac nodded his head.

"Yeah, I'll go," he said.

"Good," Jack said proudly. "But remember," he cautioned, wagging a finger playfully at his young partner. "Don't stay out past midnight, otherwise you get turned into a pumpkin!"

"I'll do my best," Mac replied, putting as much sarcasm into his response as he could.

"I'll see you tomorrow," Jack said. "Try and forget about everything except you and your lovely lady tonight," he said, pointing a finger at his friend as he stood up to walk away. Mac watched his partner walk out of the war room, and he heaved a sigh. He could only hope that Jack was right, and that all this worry was just his overactive brain trying to find the loophole in every situation.

0-0-0

"Mac?" Nikki said, putting her hand over Mac's on the table. He looked up, slightly startled.

"Sorry," he said, letting out a deep sigh. "Just got a lot on my mind," he admitted, giving the blonde woman a small smile.

"Hard mission?" she asked with a gentle expression.

"No, just thinking about something," he tried assuring his once-upon-a-time girlfriend.

"You can talk to me, Mac," Nikki said, rubbing his hand a little. Mac shook his head.

"Honestly, it's nothing," he insisted. "Let's just get back to dinner," he suggested, picking up his knife and fork to cut into the dinner their server had brought a few minutes before.

"Mac," Nikki said again, slanting her mouth and giving him a disappointed and pouty look. "You've been avoiding me ever since I got back, and I get it. I hurt you more than you ever deserved to be, both emotionally and physically," she said. "After everything that's happened in your life, I did exactly what you have always been scared of someone doing: I left you," she admitted. Her eyes filled with tears and she grasped his hand again. "I am never going to be able to apologize enough to you for what I did, but let me try to start mending our relationship," she begged. "Tell me what's wrong."

Mac observed the woman across the table from him, and a memory of a similar scene danced in front of his mind. The memory was of a diner, him and Nikki, and the table decorations he had created with the utensils they weren't going to use. The only difference between then and now was that last time, there had been agents from Nikki's organization surrounding them inconspicuously, and oh yeah. Nikki had been pointing a gun at him from under the table. He resisted the urge to check for a hidden gun, reminding himself that both of Nikki's hands were on the table, holding his. He mentally shook his head, convincing himself that Nikki was right, and that he was overreacting.

He opened his mouth to tell Nikki he had been thinking about Thornton, but another memory from the same night at the diner stopped him. This memory was of the conversation had taken place.

 _"Murdoc failed, but the next person they send won't. No one will be safe; you, Jack, my replacement...Bozer."_

Mac straightened as he realized something.

 _"Do you remember what happened to Berkhoff?"_

 _"Yeah, he was killed in exfil; his helicopter was shot down."_

 _"Who told you that? Thornton?"_

"Mac?" Nikki asked, bringing the young man back to the present. He looked at her, drawing back a little bit instinctively. "Mac, what is wrong with you today?" she asked, sounding both concerned and slightly snappy...as well as a little suspicious. Mac shook his head; he couldn't think straight-nothing was making any sense. He had to get out of there.

"I'm just not feeling very well," he informed her. It wasn't technically a lie; he was feeling confused and slightly sick to his stomach, though he knew it wasn't because of some bug. "I think I need to go home," he said in an apologetic tone. "I really am sorry," he said as he stood up. Nikki's face was a hard mask of emotions to read as she stood up with him.

"Well, I could take you home if you're feeling sick," she offered, grabbing her purse and her keys.

"No, no," he said, shaking his head and giving her a smile that he hoped didn't seem too forced. "I'll be fine to drive home; I don't want to get you sick."

"Mac, I said it earlier: I know I screwed up. I'm so sorry if it's making it hard for you to see me," she apologized again. "I want to make it up to you," she insisted. "Tell me how to do that!"

"I just...I think I just need a little more time," he finally said as they walked out the door of the diner.

"Okay," Nikki said meekly, grabbing his hand and rubbing it. "Just let me know when you think you can see me," she implored.

"I will," he promised. Nikki looked like she wanted to go in for a hug or a kiss, but Mac simply turned and walked towards his jeep. He climbed in the driver's seat and started his car, glancing at the young woman in his rearview mirror. She was staring at him with a disappointed look on her face, but he knew he had to think things through on his own, without her being there to distract and possibly persuade him one way or another. He put his jeep into drive and pulled forward, glancing back at his ex just in time to see her pull out her phone and hurriedly begin to type something. He took a deep breath.

 _I have to relax. It could be anything. I have no proof that she's doing anything besides what she says she's trying to do, which is fix whatever relationship the two of us have now. What I do have is hard, solid proof that Thornton is Chrysalis. That should be all I need, right? So why do I feel like something is wrong?_

0-0-0

Mac sat by the fire pit, staring at the dancing flames, lost in thought.

"Mac? Mac!" he heard someone calling out to him. He jerked slightly, looking up and realizing Bozer and Jack were standing there, staring at him with intense looks. "You back with us, brother?" Jack asked.

"Yeah, I'm good," MacGyver said, bringing himself the rest of the way out of his zoned-out state. Jack gave him a skeptical look, but Mac changed the subject before Jack could ask him about his date with Nikki. "You guys ready to watch the game?" he asked with somewhat-faked sounding enthusiasm. There was a football game going on, and the two teams playing were the two that Jack and Bozer both rooted for, so there was a mostly-friendly rivalry going on between them; Mac was simply there to enjoy the game.

"Oh yeah," Bozer cackled, rubbing his hands together. "Your team's going down, Jack!" he said, jabbing the older agent in the chest with a finger before he turned and walked back into the house. Jack rubbed the spot where Bozer had poked him, chuckling and shaking his head slightly. He looked back at Mac, and the blond knew the next question that was going to be coming out of his friend's mouth.

"It was fine," he lied before Jack could even voice the question. Jack quirked his eyebrows at his partner skeptically.

"See, I think I'd be more inclined to believe you if you didn't look like your favorite chemistry set had just been stolen," Jack pointed out as he sat down next to his friend. "What happened?"

"Nothing," Mac tried convincing his older partner. "We went, we ate a little, and then we left. That was it," he insisted. Jack stared at his partner, not believing him for a second.

"Come on, man," he prodded again. "How much have we been through together? And you expect me to believe that you're alright, when clearly I can see that you aren't?"

Mac sighed; he knew Jack wasn't going to let it go, so he finally decided to confide in his partner. "Just...while I was with Nikki, it reminded me of when she confronted me in the diner, after we caught Murdoc. Our conversation from that night started going through my head, and I realized something. She left Thornton out."

"What do you mean, 'left her out'?" Jack asked, brow furrowing in confusion.

"She told me that even though Murdoc failed, the next person her team sent wouldn't. She then said that none of us would be safe, mentioning each of us by name, except for Thornton."

"Okay? So maybe she just forgot to mention her," Jack argued. "That doesn't mean that Thornton's innocent," he pointed out.

"Like I said, it's just a hunch I have; I don't have any proof," Mac conceded. "But there is one more thing that isn't sitting right with me," he added, looking over at Jack.

His partner looked at him with an expectant expression. "Well c'mon, man, don't leave me hangin'!"

"That night at the diner, Nikki also brought up Berkhoff and asked me if I remembered what happened to him."

"Wait, wasn't he in the chopper that got shot down during exfil?" Jack asked in clarification.

"That's what I said," Mac agreed. "But when I said that, Nikki asked me if Thornton had told me that."

"Well, she did," Jack confirmed. "Wait, are you saying what happened to Berkhoff wasn't an accident?" Jack asked suddenly, enraged. He hadn't known the agent very well, but if Thornton had arranged for him to die, he was not going to be happy.

"I don't know," MacGyver said, trying to calm his friend down. "Nikki didn't say specifically whether Thornton orchestrated it or not. But listen," he insisted.

"Sorry," Jack said, motioning for his friend to continue.

"Nikki made it seem like Thornton was someone to be wary of months before she came out from under her CIA cover, right?"

"Right…" Jack said, realizing he could see where the kid was going with this.

"So why did she seem so shocked when we discovered Thornton was Chrysalis?"

"Maybe she had her suspicions, but she didn't want to believe them herself," Jack tried reasoning.

"So why wouldn't she just tell us her suspicions when she came out as an undercover agent?"

"Would we have believed her?" Jack asked, raising his eyebrow at his friend. Mac considered his friend's argument before he sighed, shaking his head.

"No," he admitted. "But something just isn't sitting right with me," Mac repeated, rubbing his forehead with his hand. "I can't explain what it is, but something feels wrong."

"I don't know what to tell you man, except to trust your instincts. If you think there might be something there, do a bit of digging," Jack encouraged his friend, knowing this was just going to continue to eat the kid until he did something about it.

"Thanks Jack," Mac said.

"That's what I'm here for," Jack said. "To bestow my vast knowledge on you younger generation," he added with a wink. Mac rolled his eyes, but Bozer yelled at them from inside the house before he could respond.

"Guys, are you coming?" the two of them heard Bozer yell from inside. Jack and Mac looked at each other and shared a smile. Jack stood up and held out his hand, helping his young partner to his feet, and the two of them walked inside to watch the game.

"Get ready to lose your money, Bozer," Jack said with a wicked smile. "There's no way my boys are letting me down; they're on a streak, and they aren't about to lose to some all-star wannabes," he goaded. Their (mostly) playful fighting was called off within a minute of the game starting though as all of their phones began buzzing incessantly. Mac looked at the screen, realizing it was a text from Matty to all of them. He looked at his two friends, who had concerned and slightly grim looks on their faces.

"Guess we'll have to catch this on DVR," Jack said disappointedly, reaching over and hitting the record button on the remote. "Let's get over to HQ," he said as he set the remote back down.

0-0-0

"Riley, you got the message too?" Bozer asked as they met up with the young woman right outside the Foundation.

"Yeah," she replied. "What do you think was so urgent that Matty had to call us in on a Saturday? Especially since we don't have another op for a few days," she added.

"I don't know," Mac replied as they walked in the building. "But whatever it is, Matty's text sounded urgent."

"Yeah, and it's hard for a text to sound that urgent," Jack added.

"Not for Matty," Riley pointed out.

"Yeah well, not a lot is hard for that woman," Jack argued.

"I thought you two were getting along now?" Bozer asked.

"Oh we are. Doesn't mean she doesn't scare the living-" Jack was cut off as the elevator doors opened, revealing their boss standing there, a look of both worry and frustration written all over her face.

"Good, you're here," she said, sounding more snappy than she usually did. "Took you all long enough," she added.

"Sorry Matty," Mac apologized before Jack could make a snarky remark that would probably only succeed in making their boss more agitated than she already was. "What's going on?"

"Need us to take out a terrorist cell? Is there a threat to the life of the President? Do we get to protect some lovely government women?" Jack asked, barely pausing for breath between his questions. Matty turned and stared at Jack with an unamused expression.

"No terrorist cells that I know of, the Secret Service takes care of the President, and I wouldn't put any woman through the torture of having you as their body guard," she shot at the older man. Jack put his hand over his heart in mock-hurt. "This is something more personal," Matty continued, looking at all of them with what MacGyver would almost call pity in her eyes.

"Oh no, Matty," Jack said, all joking gone from his voice. "I'm so sorry," he said sincerely, remembering what had happened the last time Matty had said that a case was more personal. Matty looked up at him, confusion and then frustration coming over her face.

"It's not personal for me," she clarified. She stared at the four confused and slightly worried agents around her. "I just got a call from the CIA facilities that Thornton was being held at."

Mac's gut sank, and he knew what the next words out of her mouth were going to be even before she said them.

"Patricia Thornton has escaped custody."

 ** _Ah, but did she really escape, or did something more sinister happen? 0.0_**


	2. Chapter 2

_**Here is chapter two!**_

 ** _I own no part of this amazing show :(_**

"Escaped?" Jack asked, his jaw hitting the floor. "What do you mean 'escaped'?"

"I mean she's gone. What else would I mean?" Matty snapped at him. "From what they told me over the phone, it looks like she had help. They don't know if it was an inside job or not, so they're trying to check out as many people as they can who work at the CIA, paying special attention to the people who worked at the prison, as well as anyone who might have had anything even remotely to do with Thornton."

"That includes Nikki?" Mac asked, though he already knew the answer.

"Yes," Matty confirmed. She gave MacGyver a strange look when he asked about his ex, but she didn't press the matter.

"Wait, are we being looked at too?" Riley asked, sounding slightly incredulous.

"It does, but they assured me it was just more of a formal thing; they know the background of what happened with you guys and Thornton, and they know you didn't help her escape; they're just wanting to cover all grounds. Don't worry- I won't let anything happen to anyone who doesn't deserve it," Matty assured them.

"So what exactly are we supposed to do now?" Riley asked.

"For now, it's all hands on deck," Matty replied. "We're going to the holding facilities where they were keeping her, and I'm not leaving until we find something."

0-0-0

"Here it is," the guard said as he led them to Thornton's cell. Things looked neat and orderly, and the sight gave Mac's gut a pang as he had flashbacks of how organized his old boss had been, even while off work. There was a small bed in the corner, with a book laying on top of the blanket.

"Can I take a look at your security camera feeds?" Riley asked, pulling Mac out of his nostalgic zone.

"Wish you could, but all the footage that contained the prisoner within the last forty-eight hours have been corrupted," the guard admitted.

"Why would they corrupt the drive?" Mac asked, getting a gnawing pit in his stomach that wouldn't leave him alone.

"Probably so that they could keep the identity of whoever helped Thornton escape a secret for at least a little longer. Y'know, give them more time to get a good distance between them and any law enforcement officer," Riley reasoned. She turned back to the guard. "Mind if I take a look at them anyway, see if I can salvage anything?"

"Be my guest," the guard said, motioning for her to follow him. "Dunno what you think you're gonna be able to see though."

"I won't know until I see the tapes," Riley replied, her voice fading as the two of them got further and further from the cell.

Mac wandered around the small room, scanning everything he could. He noticed something on the floor by Thornton's bed, and his eyes narrowed a little bit. He turned around, looking back over the room with a renewed vigor before walking over to the bed.

"Mac?" Jack asked, confusion etched in every part of his expression as he watched his partner crouch down near Thornton's bed. "What's goin' on?"

"A jail break usually happens rather willingly, right?"

"Uh, yeah, that's usually the way things go down," Jack agreed, not seeing where his partner was going with this line of questioning. Mac motioned for Jack to come closer, and when his friend complied, Mac pointed to something on the floor.

"If that's the case, then why is there blood on the ground?" Mac asked, staring at his partner with a serious expression.

"I dunno, maybe they conked noses or something when he bent down to undo her leg restraints," Jack mused, though he didn't sound extremely convinced by his own argument.

"First, why would she be wearing restraints in her own cell?" Mac pointed out. "And second, you and I both know that's not as likely as there being a scuffle and things getting physical," Mac said.

"Look dude," Jack conceded. "Say you have a point and this breakout wasn't voluntary. Where does that leave us? Riley's doin' her best with the security cameras, but even she has a hard time when the drive is completely corrupted," he pointed out.

"It leaves us with a blood test to run," Mac said. "That's a start; that's our scrap of actionable intel."

"Well, let's get it over to the labs, have them do their thing," Jack said.

0-0-0

MacGyver, Jack, Riley, Bozer, and Matty were all sitting in the war room, going over the little evidence they found in the cell. There were pictures of every part of the tiny room, and everything that could be moved had been taken to the Phoenix Foundation as evidence. The book that had been on Thornton's bed was currently in the labs, being examined for any sign of tampering, like invisible ink on the pages and the like to see if Thornton was having communication with the outside world. The five of them were staring at the screen when someone opened the door and stuck her head in.

"Ma'am," the woman interrupted hesitantly.

"What is it?" Matty asked, turning to look at the young woman.

"The results for those blood tests you ordered came back," the lab worker replied.

"And what do they tell us?" Matty asked as she walked over to accept the tablet the lab tech was holding out.

"There were actually two different sets of DNA from the blood samples that were gathered," the woman explained. "One belonged to Patricia Thornton, but the other belonged to a John Anderson; he was a security guard who worked at the prison."

"Thank you Elyssa," Matty said. Elyssa nodded her head and ducked out of the conference room. Matty looked at the agents surrounding her. "That doesn't prove anything," she said, seeing the look on her agent's faces. "It just shows that she had outside help, that's all," she insisted. "There is no solid proof to back Blondie's theory here that she was captured," she added. "Besides, what would anyone's motive be to kidnap the mole? She's already in prison for life, what more could someone want?"

"Maybe someone wants her more than locked up," Jack suggested, trying not to sound too ominious. Mac chewed his bottom lip, wanting to pose his theory about Thornton's innocence, but he knew he didn't have any proof whatsoever to back up his idea, and Matty wouldn't be willing to listen to the idea without hard evidence to back it up.

"Why would anyone want her dead?" Matty asked, only slightly condescendingly.

"Maybe her activities as Chrysalis ruffled the wrong feathers," Jack defended. "We know not everyone Chrysalis came into contact with was lucky enough to walk away," he reminded everyone. He felt terrible saying the things he was saying, especially when he knew Mac was having a hard time believing whether Thornton was guilty or not, but he figured that proving she had been kidnapped instead of escaping of her own will was a solid place to start.

Matty stared at Jack for a few moments, mentally chewing over his argument in her head. "Find everyone who has had someone die as a result of Thornton's actions," Matty ordered after she considered Jack's reasoning. "I wanna know anyone who might have a possible motive to want her dead. Start with anyone who has a connection to the guard, Anderson," she added. Everyone nodded, but when no one moved, Matty glared at all of them and held out her hands in exasperation. "Well?" she asked. "Are you going to go find Thornton, or are you stand there staring at me all day?"

Everyone jumped as if they'd received an electrical shock and began dividing, doing what they could to try and find Thornton. Mac walked out of the war room with a contemplative look on his face. Jack saw his friend's expression and followed him out.

"Mac, what are you thinking?" Jack asked quietly as they walked away from Matty, even though he had a hunch he already knew what was going on in his partner's brain.

"I'm thinking there's more to this story than we originally thought," Mac replied. "You and I both know that no one broke her out of prison to get revenge," he said.

"Yeah, that's what I said in there," Jack reminded the kid. "So what are you sayin', bud?"

"I'm saying that I think we should take another look at the files that were used as evidence against Thornton."

"What do you think we're gonna find?" Jack asked. "We've had our best analysts go over everything, and they weren't able to crack any of the codes used by Chrysalis and her people," the older agent reminded his young partner.

"I don't know," Mac admitted in slight frustration. "I don't even know why I'm having all these second thoughts," he added. "I should just forget about it; we have the proof Thornton is guilty, and she hasn't tried to convince anyone otherwise," he said. "Why do I think she's innocent?" he asked, looking at his friend slightly helplessly. Jack studied MacGyver for a minute before turning and calling out to Riley.

"Hey Riley, could you come here?" he called out. The young hacker, who had been walking down the hallway, turned and made her way back to the two men.

"What's up?" she asked as she approached them.

"Ri, what happened to the evidence that was used against Thornton?"

"Um, I'm pretty sure it was just filed away," she said, shrugging her shoulders.

"Filed digitally?" Jack clarified.

"Yeah, the stuff that we could file digitally...why?" Riley asked. Jack looked up and down the hallway for Matty, and when he didn't see her he led the two younger agents back into the war room and shut the door. He gestured for Riley and Mac to sit down, and he took a seat on one of the leather chairs as well. Riley remained standing, not entirely sure about what was going on still.

"Think you could sneak around and pull up any files or evidence used on Thornton?" Jack asked.

"You think that's gonna help us find her?" Riley asked skeptically.

"We're not exactly sure what it's gonna help us with," Jack answered honestly. "Just a hunch Mac has," he explained. Riley continued to give him a confused and slightly suspicious look, but she finally sat down and pulled her laptop out of her backpack.

"I'm assuming you want to keep this little peek into the evidence a secret?" the young hacker asked as she began typing away on her laptop.

"That would be appreciated, yes," Jack confirmed. He grinned; he knew they could count on Riley, and he knew that if she didn't want to be found sneaking through the evidence, she wouldn't be.

"Hey," Mac said as Riley began typing. "Could you also find and pull up anything you can on Agent Berkhoff?" he asked, deciding to play his hunch and see if it panned out anywhere. Riley gave him another slightly puzzled look, but she nodded and continued typing.

"Do I get to know what I'm breaking at least half a dozen Phoenix rules for?" she asked after a few minutes, sparing a second to glance over at the two men sitting around her.

"I'm just wanting to double check and make sure we got everything right," Mac explained.

"Mac, I know how much Thornton meant to you, but it sounds like you're chasing ghosts," Riley commented, pausing in her typing for a minute to look at the blond. Mac saw the pitiful look in her eyes and knew he sounded like he was crazy, but he couldn't shake the feeling that something wasn't right.

"I know," Mac assured her. "And I'm not saying that we're going to find anything; I just want to take a look."

Riley considered the boy a moment more before nodding, and she began typing once more. They sat there for a few more minutes in silence before Mac's phone began ringing. When he looked down, he saw it was an unrecognized phone number flashing on the screen, and he had a weird feeling in his stomach as he accepted the call. "Hello?" he asked.

"Mac, I need your help."

 _ **I'm just gonna throw this out here, I've been working on this story for about two and a half months now, just playing around with ideas in my head, so to me, things kinda seem jumbled and mixed up and slightly crazy/OOC to me... Sometimes I can't even see the story/words straight, so please let me know if things don't make sense or seem OOC? In a constructive way though XD If I get flames, I won't answer.**_

 _ **I just read and re-read things so often that my stories seem boring to me, so I'm hoping they don't seem that way to you, but... *shrugs* maybe they are boring and you guys are just too nice to tell me to stop writing XD**_

 _ **Anyway. Small rant/explanation over, sorry 'bout that XD I'm just really tired and so ready for school to be over, so that's leaking out in my ANs now XD**_

 _ **Lemme know what you think!**_


	3. Chapter 3

_**Chapter 3! Guys, I'm so glad you're all enjoying the story so much! Thank you all! *massive hugs all around* Longer AN at the bottom :)**_

 _ **I don't have anything to do with MacGyver**_

Mac's eyes widened, and he immediately stood up and walked away, drawing confused looks from Jack and Riley. "Hey, Pete, how's it goin'?" he asked, trying to sound as casual as he could. He exited the war room, but still lowered his voice to a whisper so that Jack and Riley couldn't hear what he was saying.

"Thornton?"

"Mac, I know I'm the last person you expected to hear from-"

"You think?" he said sharply, his voice rising slightly. He glanced at his friends and saw Jack staring at him, so he walked a little further away and lowered his voice again. "Why shouldn't I just tell everyone you called, and let Riley trace whatever number you're calling from?" he asked, raising his eyebrows as if his former boss could see.

"Don't you think I would have considered the possibility that you'd do that?" Thornton asked, her voice sounding slightly strained. "I knew there was every chance in the world you might do that, but I took the risk anyway. Mac, if I had broken out of prison on my own, I would be long gone, wouldn't I?" she asked, trying to reason with the young man. Mac considered this for a minute.

"Unless you're just trying to lure me somewhere to kill me," he pointed out. "We all know what you tried to do in Amsterdam," he added, though he didn't sound as confident as he had hoped he would when he said that.

"Mac, that wasn't me," Thornton said. "Please, just hear me out," she said, her voice almost begging.

"I can't trust you," Mac replied simply. "I shouldn't even be having this conversation!"

"Please, Mac," Thornton said. MacGyver was a little surprised. In all the time he had known Patricia Thornton, he had never known her to sound this desperate. "Mac?"

"I'm still here," he finally said.

"Look, I know you have absolutely no reason to trust me," Thornton said. "But I need your help."

Mac exhaled through his nose as he weighed his choices. He thought back to everything that he had been arguing with Jack about, and about his feelings with Nikki. He realized that this was the chance he had been looking for to get answers about Thornton once and for all; besides, Thornton had been there for him and the team so many times, he figured he owed her at least the benefit of talking to her.

"Where are you?"

Thornton requested that they meet in a less-populated part of the city, and while MacGyver felt a little uncomfortable, he also understood that she probably didn't want much attention drawn to herself. Once he got the location where she wanted to meet, the phone call was disconnected, and Mac stared at the phone in his hand with a tormented look on his face.

 _0-0-0_

Jack's eyes narrowed as he watched his partner walk away to take his phone call. Riley switched her gaze between the two men, confusion written all over her face.

"Why are you glaring at him like that?" she asked Jack.

"I just get the feelin' that something's not quite right," Jack explained. He watched his partner for a few more minutes until finally the blond withdrew his phone from his ear and stared at it with a tortured expression. Jack stood up and strode towards his friend, intent on finding out what was going on.

"Hey man," he said as he exited the war room and approached the blond.

"Hey," Mac replied, somewhat disjointedly.

"What was that?"

"Nothing, just an old...friend," Mac finally said.

"You board the lyin' train recently or somethin'?" Jack asked in frustration. Mac looked at the older agent with a look that Jack assumed was supposed to be innocent, but definitely looked more like the younger man was trying to hide something.

"There's no such thing, Jack," Mac finally said, trying to derail his partner's interrogation.

"There wasn't until you created it," Jack replied. "Back when you started lyin' to me about what's been eatin' ya the night you had your date with Nikki," Jack shot back. "I know you kid. Something just happened. Plus, I've heard you talk about all your friends before, and I've never heard mention of a 'Pete'."

Mac's mouth opened and closed a few times, and a few attempts of more lies came out of his mouth, but Jack cut him off with a pointed stare. "Tell me what's goin' on, man," Jack insisted. Mac's mouth pressed into a thin line.

"I don't know how to say it," he argued.

"It's easy. Y'know how we're speaking right now? Just do the same thing, but this time, the words that come outta your mouth will be the name of the person who was on the other end of that phone call," Jack explained sarcastically. Mac glared at the older man, but he finally gave in. He looked around them cautiously to make sure they wouldn't be overheard before he leaned closer to Jack.

"It was...it was Thornton," he admitted quietly.

"Thor...it was Thornton?" Jack asked incredulously, lowering his own voice before he drew attention to them. "Dude, we need to report this to Matty or someone," he insisted.

"I don't know…" Mac said hesitantly.

"What do you mean you don't know?" Jack asked. "Even if you're having second thoughts whether Thornton is guilty or not, the fact still stands that she's escaped prison," Jack reminded Mac.

"But it might not have been her choice," Mac argued. "You're the one that said to go with my gut," Mac reminded Jack.

"I did, but I'm also telling you now to make sure that you're sure you want to go down this path," Jack said. "Once you go down, it'll be a lot harder to come back, if it's even possible."

"That may be," Mac admitted. "But if I don't do this, I'll always wonder, and I'll just beat myself up thinking 'what if'."

Jack stared at the blond. "You're gonna do this no matter what I say, aren't you?" he asked.

"I have to know," MacGyver said apologetically.

"Okay," Jack said, shrugging.

"Okay?" Mac said. "That's it? No more lecturing about...anything?"

"Nah, I'll save those for later," Jack assured his partner. "But I'm comin' with you," he added. MacGyver opened his mouth to argue, but Jack held up his hand and stared the blond down. "I'm with ya all the way on this, bud. Let's go do something stupid."

 _0-0-0_

"I can't believe we're doin' this without any backup, man," Jack complained quietly as they waited.

"You're the one that said you wanted to come do this," Mac reminded him. "Besides, we're each other's backup," he added slightly distractedly as he looked around, trying to spot Thornton. The two of them had agreed to this part of town because it wasn't very crowded, and there was less of a chance that she'd be recognized, but it still made MacGyver uneasy. "Besides, what were your exact words? 'Let's go do something stupid'?"

Jack didn't respond, but Mac wasn't really paying attention to the older man at the moment anyway. He was too busy looking around, trying to find any sign of Thornton.

 _I'd never tell Jack this, but I'm really glad he came with me. If this does turn out to be a trap, I was serious when I said we were each other's backup. Hopefully this isn't a trap though, and we won't have to worry about backup._

A few more minutes passed by with nothing happening, and finally Jack looked at Mac. "Dude, I don't think she's coming, which more than likely means this is a setup. Let's get outta here before Thornton's people show up and kill us both," he insisted, pulling at Mac's sleeve. Mac began to answer him, but stopped as he spotted some movement a little ways down an alleyway slightly to their left. He pointed it out to Jack, who nodded, letting his friend know he had spotted the movement as well, and the two of them made their way towards the shape in the shadows.

As they got closer, they both recognized the lean figure leaning heavily on the wall for support. She had stripped her orange jumpsuit down to her waist, leaving a white undershirt underneath, and she had tied the arms of the jumpsuit in front of her to keep it up, almost looking like the people who tied sweaters around their waists.

"Thornton?" Mac said, quickening his pace. Their former boss looked up and saw them, and her face took on what Mac could only assume was a relieved expression, mixed with quite a bit of pain. She had a large cut on her forehead, which is where Mac figured the blood left in the cell must have come from, but what was more concerning to him was the way she was holding her side, as well as the crimson color her fingers were painted in as she clutched at her side.

"What happened?" Mac asked, hurrying the last few steps to his former boss to help her sit down on a crate that was against the wall.

"Got shot," she muttered as she closed her eyes.

"Thanks for pointing out the obvious," Jack snarked. Thornton opened her eyes a little to glare at the older agent, and for a minute Mac felt like they were back in the time before Thornton turned traitor.

"What happened?" Mac asked again as he began to examine the wound.

"When I was grabbed from my cell-"

"You mean when you escaped?" Jack interrupted.

"It would be a lot easier to tell you what happened if you actually let me speak," Thornton reminded Jack drily.

"Sorry," Jack said, holding up his hands in surrender.

"When I was grabbed, I tried to fight back," she began, gesturing at the cut on her forehead. "But they injected me with something, and I don't remember anything else until I woke up; by that time, we were on the road. They had put a bag over my head, and I'm assuming I was in the back of a van. We stopped and they hauled me out, but they made the mistake of only leaving one guard with me, and he made the mistake of taking his eyes off me for too long. Didn't get away cleanly though," she said, referring to her side.

"The question is, who broke you out, and why do it in the first place?" MacGyver asked, almost to himself.

"I don't know. If I had to hazard a guess, I would say it was whoever framed me as Chrysalis. As for the why, I can only think it was because they somehow heard that I requested to speak to you," Thornton mused before giving a sharp gasp as Mac examined her wound.

"Sorry," Mac muttered, chewing his bottom lip as he gave the woman an apologetic look.

"Why wouldn't they just kill you?" Jack asked. "Sorry for the bluntness," he added. "I just...why go through the trouble of breaking you out, when they could just as easily have slipped you something that made it look like you died of natural causes?"

"It's a valid question," Thornton said, breathing heavier and heavier with each breath she took in. "I think because if I died, there would be an autopsy, a chance for them to find out it wasn't natural," she said. "By breaking me out and making it look like I escaped, they discredited me even further."

"Well, we suggested the idea that someone broke you out to get revenge for your activities as Chrysalis," Jack supplied. Thornton raised her eyebrows but didn't say anything, and Jack continued. "Why did you want to talk to Mac anyway?" he asked, sounding slightly suspicious.

"I had someone looking into the evidence gathered on me proving that I was Chrysalis," she said vaguely. "My guy found something; a crack in the case that was built against me. It's not enough to prove I'm not Chrysalis, but it's a start. I was going to ask Mac to look into it further, but obviously things didn't quite go according to plan," she finished, looking at their surroundings.

"So why didn't you just have your person go to someone more powerful with this intel?" MacGyver asked.

"I know this is going to sound paranoid, but I don't know who I can trust," Thornton admitted. "You two, Riley, and Bozer are the only ones I trust right now."

"Okay, follow-up question," Jack interjected. "Why didn't you go to the cops yourself once you got away from whoever broke you out of prison? Y'know, turn yourself back in?"

"I couldn't go to the cops," Thornton said, as if it were the simplest thing in the world. She hissed a little as MacGyver prodded her wound, and he muttered another apology.

"Why?" Jack asked, crossing his arms. "Running makes you look more guilty."

"Trust me, if it would help me stay alive, I'd do it in a heartbeat," Thornton promised. "But they were going to kill me. I saw the chance to get out and took it, but they got me anyway," she said, indicating her injured side gingerly. "I don't know how many people The Organization has on its payroll, but I know it spans across all forms of government; the CIA, FBI, police, and I _know_ they have more people at Phoenix. I can't trust anyone in the police department. If I got placed in the wrong hands, they might just call The Organization, and I'd be dead faster than you could say Chrysalis."

"Why couldn't you just tell us what happened, tell us you were innocent?" MacGyver asked. "You didn't say anything when you were arrested, which made it seem like you were just upset you had been caught."

Thornton looked at him with a raised eyebrow. "Whoever it was that framed me as Chrysalis did enough homework and put enough time and effort into their findings to make sure that for all intents and purposes, I _was_ Chrysalis. Even I was tempted to believe it when I saw all the evidence that had gathered. I knew I had to get enough proof of my own together before I involved any of you. Otherwise, even if you believed me, I doubt anything would have stuck."

"Why didn't you ask Riley to find anything?" Jack asked, almost accusatorily.

"Jack, she just said she didn't want to get us involved unless she had something concrete," Mac reminded his partner.

"I didn't want any of you involved because I knew if any of us were caught, it could be damaging to you and your careers," Thornton expounded. "I knew someone who could help; he owed me several favors. I cashed them all in, and it paid off."

"So he found evidence to prove that you're innocent?" Mac asked, stopping his examination. "Where is it?"

"Safe," Thornton replied. "And I'm not exactly sure what he found; all he told me was that he found _something_. You have to talk to him. He's the only one who knows what and where it is. That way if we were compromised, The Organization wouldn't be able to find whatever evidence he had gathered and destroy it."

"That's convenient," Jack commented. MacGyver gave his partner an exasperated look.

"Jack, it seems like there's more to the story. Why are you so against this?"

"I dunno man. Something about trusting people who betrayed us once just doesn't sit right with me," Jack replied.

"You trusted Nikki finally," Mac pointed out.

"True," Jack conceded. "But remember how long that took?" he reminded Mac. The blond sighed and nodded, and Jack looked at Thornton. "Besides, how do we know this isn't just a really elaborate plot to get Mac out here alone so you could kill him?" Jack pointed out.

"You really think I'd have someone shoot me in the side to make my story seem more believable?" Thornton asked tiredly.

"Well if you really _are_ Chrysalis, then you're the one who ordered the hit from Murdoc, and you had him shoot you in the shoulder," Jack pointed out. "What's another shot to the side?"

"Jack," Mac said in a low, almost warning voice.

"No, he's got every right to be suspicious," Thornton said, a pained expression crossing her face when Mac continued to look at her wound.

"No, I mean Jack needs to shut up, because even if you did have them shoot you to make you seem more innocent, I think the bullet pierced your kidney," he said, sitting back and looking at Thornton with a concerned look in his eyes. Jack's face lost some of its hardness when he heard that, and he hurried over to examine the wound as well.

Thornton's upper abdomen was a blanket of black and blue, and Jack could also see bruising between her ribs and hip. He looked at his partner, and knew they were both thinking the same thing.

"Patty, we gotta get you to the medical center at Phoenix," Jack said, the suspicion gone from his voice, replaced with worry. Thornton shook her head, but before anyone else could say anything, the three of them heard yelling and the cocking of guns.

Mac stood and turned around quickly, but he wasn't able to do anything as CIA agents swarmed the alley. MacGyver and Jack were pushed up against the wall face-first with their arms twisted behind their backs, while other agents surrounded Thornton. MacGyver and Jack struggled against the men holding them, but the grips only tightened.

"You can let them go," a familiar voice said. The two agents were released after another minute, and they both turned to face Matty, who was walking down the alley towards them. "I've got it from here," she promised the agents who had just released the two Phoenix agents. "Make sure Thornton gets to the hospital," she added as she saw the dark-haired woman and her bloody undershirt. The men nodded and walked away, leaving Matty with her two agents. She looked at them in anger.

"You two have some explaining to do."

 _ **Uh-oh...**_

 _ **So thoughts? I know Thornton seemed a little OOC to me, but I figured she's in pain, she's running, and she's tired, and that can make anyone act differently. Sorry if it was too OOC though...**_

 _ **Okay, did anyone catch my pun earlier in the story? :D It was totally unintentional, but once I found it I vowed I wasn't going to take it out XD Also, yes there is a very blatant throwback to the old MacGyver series...anyone catch that? ;)**_

 ** _Anyway! Lemme know what you guys thought!_**


	4. Chapter 4

_**Hey hey hey! Kk, a bit of**_ _ **housekeeping**_ _ **:**_

 _ **First off, just wanted to let you all know how thankful I am for all of you! You're all the best!**_

 _ **Second, helloyesimhere asked me to let you all know that she won't be updating any of her stories for a little bit except for maybe 'The Life and Times of MacGyver & Co' because she has family in town! **_

_**Third, does anyone else find it sad that there's no MacGyver tonight? *lowkey cries***_

 _ **Fourth: onto chapter Four!**_

 _ **I own nothing of these characters :(**_

"You bugged my phone?" Mac asked angrily, staring at his boss incredulously. When they had reached the hospital, MacGyver had wanted to find out how the CIA and Phoenix Foundation found him and Thornton, seeing as how he took great trouble not to be followed, and had even turned _off_ his phone so that it couldn't be tracked. That didn't matter though, because from the get-go, it seemed everyone had known where he and Thornton would be meeting.

"I didn't know anything about it, blondie!" Matty snapped back. "I only found out they had done it when we rolled out. Don't accuse me of things that you don't know for sure are true," she admonished.

"Just like people are doing to Thornton?" the blond snapped. Jack stared at his partner; this wasn't like Mac at all.

"We have solid evidence proving that she is Chrysalis!" Matty shot back.

"But what if the evidence is fake?" Mac argued.

"What makes you think that?" Matty asked skeptically, crossing her arms.

"Thornton has a guy-"

"Oh, she has a guy?" Matty asked crossly. "Is that supposed to make me suddenly change my mind? Do you know who this guy is? Do you know what his evidence is? Do you even know _where_ he is, or where he's keeping this supposed 'evidence'?" she asked, glancing between the two of them.

Mac and Jack mumbled a bit, but neither of them were able to give a definite answer.

"Well, until you can make this 'guy' appear, Thornton's staying in custody," Matty said firmly. MacGyver didn't look happy, but he knew that Matty had a point; they needed to find Thornton's man and whatever evidence he had before they could figure out of she was innocent or not. He tried to keep the frustration out of his voice as he changed topics.

"What's going on with Thornton? How's she doing?" he asked.

"She just got out of surgery," Matty explained. "The bullet had pierced her kidney, but the doctors were able to stop the bleeding and repair the damage with little trouble. She's in recovery right now, then she'll be moved to a secure room until the doctors clear her to be taken back to prison. She's got one armed guard outside her room currently, but once she's moved out of recovery, she'll have two guards outside and one guard inside. She's not going anywhere."

"I need to talk to her," Mac insisted, trying to step past to get to his old boss's room.

"Hold it, Mac," Matty said, stepping in front of him and holding up her hand. "You're not out of the woods yet. You had contact with a wanted fugitive and didn't tell anyone," she reminded him.

"Well, that's not completely true; he told me," Jack pointed out. MacGyver shot his partner a very annoyed look; he was trying to keep the older man out of this as much as possible.

"Jack, if I were you, I just wouldn't talk," Matty said rather tersely.

"Matty-," MacGyver began, but he was cut off.

"I'm sorry, Mac," Matty said. "I'm going to need to ask you to stay home until we can figure out how to deal with this. I don't want to make it a direct order, but I will if I have to," she added.

"Matty, at least let me talk to Thornton," Mac begged.

"I can't allow you do that," she said. Mac's face fell, and she stared at him for a minute longer. "I'm going to go talk to the doctors," she finally said, giving them a knowing look. "When I come back, which will be in about five minutes, I want you to be gone, and MacGyver," she said, staring straight at him. "I don't want you to leave your house until I say you can," she instructed.

"What about me, Matty?" Jack asked as their boss turned to walk away.

"Did I say anything about you being under house arrest?" she asked, turning back to face them briefly. The two of them got the message loud and clear. They would be able to talk to Thornton while Matty was away, and though Mac was going to be stuck at his house, Jack would be able to chase down any leads that Thornton's guy could give them.

As soon as she began walking away, MacGyver and Jack made their way towards Thornton's recovery room. "Look dude," Jack started quietly as they walked quickly down the hallway. "I know you're fired up about this, and the more I think about it, the more I agree with you that there is something weird going on here, but ya gotta tone it back a bit, bud," he said, trying to stress how important it was that Mac keep his cool. MacGyver nodded, almost imperceptibly, but at least Jack knew that his partner had heard what he said, and would hopefully take at least some of it to heart.

When they neared Thornton's room, they saw a guard standing outside, just like Matty had said there would be. Mac knew that they wouldn't be able to convince him to let them in to see her, but before Mac could even think of thinking of an idea to get them past the guard, Jack pulled his young partner back around the corner, out of sight of the guard.

"Okay, I'll provide a distraction, you just gotta sneak in there and get the name of Thornton's guy," Jack said.

"You?" Mac asked, raising an eyebrow at his friend. "You're going to provide a good enough distraction that I can get in the room, get the information from Thornton, and then get out before he notices?"

"Yeah, well, I never said your part was gonna be easy," Jack said, shrugging at his young friend. Mac stared at his friend in exasperation, but before he could say anything else, or suggest a different plan, Jack took off around the corner, whistling quietly as he went. Mac leaned against the wall until he heard Jack begin talking. Once he heard his partner's voice, he peered around the corner, making sure the guard's back was turned before he quietly snuck down the hallway. Once Mac neared the door, Jack raised his voice slightly to cover the sound of his friend's footsteps. Mac reached the door, and Jack suddenly exclaimed something about the smell of a hospital making him physically sick, and he bent in half, grabbing the shoulder of the guard and dragging him down partway, giving Mac the opportunity to slip into the hospital room unnoticed.

He quietly shut the door and hurried over to Thornton's bed. The dark-haired woman was staring at him, her wrists cuffed to the side of the bed. Her eyes were slightly unfocused and Mac could tell she was on some heavy pain meds. He knew he only had a limited amount of time before the dark-haired woman fell asleep, so he walked closer and opened his mouth to ask about Thornton's guy.

"Charles Conway," Thornton answered before the blond could even voice his question.

"Wait, how did you know-"

"Why else would you be here?" she asked, raising an eyebrow at Mac. "Besides," she continued. "I recognized Jack's distraction voice," she said drily. Despite the situation, Mac couldn't help the small grin that broke across his face.

"I guess it's pretty distinctive," he agreed. Thornton's mouth quirked up a little.

"Just a little bit," she replied tiredly. "Listen," Thornton said, pulling herself up slightly to stay more alert. "This is the number you need to get ahold of Charles," she said. Mac grabbed a pad of paper from the bedside table, along with a pen. He wrote down the number Thornton recited and ripped the page off the notepad, stuffing it in his pocket.

"When you find Conway, tell him what happened, and tell him that the queen needs her court defended," Thornton continued. MacGyver raised his eyebrows at her in confusion. She shook her head. "I'll have to explain later. You need to leave now," she added.

"Right," Mac muttered, turning around and striding towards the door.

"Mac," Thornton said as he reached for the handle. MacGyver could hear Jack outside beginning to lose control of the situation, but he turned his head to face his ex-boss anyway. "Take a closer look at Agent Berkhoff's file," she instructed. Mac stared at her for a minute, the memory of his conversation with Nikki flashing through his mind.

" _Why would Thornton be asking me to look into the file if she was trying to hide something?"_ he thought to himself. He gave a quick nod to let Thornton know he understood, and her eyes filled with relief, even as they drooped in exhaustion.

"Thank you," she said sincerely. MacGyver gave her another small nod before reaching out and grabbing the handle. He pulled the door open as quietly as he could and snuck out from behind the guard's back, which was still to the door, thanks to Jack's distraction abilities. The entire encounter with Thornton had taken two minutes or less, but Mac felt like it had lasted an eternity.

Jack saw his partner sneak out the door, and waited until the kid had disappeared around the corner before clapping the guard on the shoulder and walking away, feeling proud that he had distracted the guard enough for Mac to get in and out without being noticed. The guard stared at Jack suspiciously, but he didn't raise the alarm, much to Jack's relief.

Jack walked briskly down the hallway, trying not to draw anymore attention to himself than he already had, and he let out a relieved breath when he walked around the corner and no one tried to stop him. He saw Mac a little ways ahead of him and hurried to catch up.

"Hey," he said as he pulled up next to the blond. "So? What'd she say?"

"Come by the house as soon as you can," Mac said. "Bring Riley too," he added.

"You got it," Jack agreed. The two of them heard Matty's voice coming down the hall, and Mac knew his five minutes were up, and that he needed to leave immediately. The blond skirted around the corner right as his boss came down the opposite hallway. Matty looked up and saw Jack standing there, and she watched as he gave her a small, almost unnoticeable nod; she briefly raised her eyebrows to show that she understood, and turned to continue talking with the doctor.

 _0-0-0_

MacGyver walked down the street with his hands in his pockets and his head low, keeping an eye out to make sure he didn't have a tail. He was going to follow Matty's orders and go home, but he had no way of knowing if his phone calls were still being listened to, and he needed to find a phone he knew would be free of prying ears. As he walked down the street, he finally spotted a payphone. He hurried over to it and pulled out the paper he had scribbled the number on, looking all around him to make sure he wasn't being watched.

He inserted a few coins and punched in the phone number before putting the phone to his ear. After two rings the call was answered; the voice on the other end was gruff, and sounded rather upset as they spoke.

"I don't know who you are or how you got this number, but you've got exactly twenty seconds to tell me why you're calling before I hang up," the voice said. "Your twenty seconds started as soon as I answered this call," the voice added. Mac's eyes widened, and he spoke quickly.

"My name is MacGyver, and I need your help. The queen needs her court defended," he said, trying his best not to stumble over his words as he quickly repeated Thornton's message. There was no answer for several seconds, and MacGyver frantically tried to remember if he had said the phrase correctly. He was about to say something else to make sure the man was still on the line, but he didn't have to.

"I will meet you at your place in twenty minutes," the voice said, still sounding gruff, but not nearly as upset. Mac opened his mouth to give the man his address, but the call was disconnected. Mac stared at the receiver in bewilderment, and he considered calling the man back, but he thought better of it. Something in Conway's voice let Mac know that he didn't need instructions to find Mac's house.

While that thought was a little disturbing, Mac didn't dwell on it as he began to make his way home. It was only about fifteen minutes walking distance from his current location, but Mac kept a brisk pace anyway, not wanting to even run the chance of being late and missing the man who supposedly had the answers to figuring out whether Thornton was innocent or not once and for all.

 _ **Okay! Whatcha all think?**_

 _ **Also, I'm going to try to update again on Sunday morning, but I'm going home for the weekend as soon as I'm done with my one class today, and I don't know if I'll be able to. I think I should be fine, but I'm just putting a warning that I may not be able to update again until Monday :)**_

 ** _Let me know what you think!_**


	5. Chapter 5

_**Hello my lovely friends! I'm so happy I was able to post this morning :) Okay, longer AN at the bottom :)**_

 _ **I don't own anything to do with MacGyver**_

Mac was sitting on his couch, staring at the computer in his hands with an expression that was hard to read. Some may have called it relief, some may have called it sad; there would also be those who called it a mix of both. There was a man in a cowboy hat sitting on the couch across from him, staring intently at the blond as he studied the information he had just been handed. Mac was jerked out of his intense staring contest with the computer screen when he heard his front door open, and Bozer walked in.

"Mac," his roommate said. "Jack said something about you being under house arrest?" Bozer pulled up short as he saw the other man sitting on his couch, but MacGyver didn't even seem to notice his friend's inquisitive look.

"Long story," Mac said, waving off his friend's confusion. "Where is Jack?" he asked, looking behind Bozer as if Jack was hiding behind the newest Phoenix agent.

"He said to tell you he'll be here in like five minutes," Bozer relayed, still staring at the newcomer, who was staring at right back at Bozer with an unfazed expression. "He was right behind me when I left."

As if on cue, Jack opened the door and stepped through, followed by Riley.

"You got sidelined?" Riley asked incredulously as she saw Mac sitting on his couch. Jack opened his mouth to say something, but just like Bozer had, he stopped short when he saw the stranger sitting on the couch.

"I did, but that might be just what we need," Mac said, drawing even more confused looks from all his friends.

"Sorry, how does you being grounded equal success for us?" Bozer asked, tearing his eyes away from the stranger on the couch.

"Now I can put all the time and effort I possibly can into sifting through this evidence and find anything to help prove Thornton is innocent," Mac explained.

"Wait, what?" Bozer asked.

"Say what now?" the young hacker asked in disbelief.

"Yeah, we were going to tell you," Mac told them. "But I think there's more to the Thornton story than we originally thought."

"I knew you were wanting that evidence for something, but _when_ exactly were you planning on telling us this?" Riley asked, sounding more than a little cross.

"I guess as soon as we found proof," Mac admitted, bracing himself for the torrent of anger that he was sure was going to be coming his way, but neither Bozer or Riley yelled at him. They simply stared at him with annoyed and slightly hurt expressions, which almost made Mac feel worse than if they had yelled at him. "Could we maybe save the guilt-tripping for later?" Mac requested as the staring contests continued between the three of them.

"We _will_ be having a conversation about this later," Bozer said in as much of a threatening tone that he could muster after a minute more of staring at his roommate.

"Fair enough," Mac said.

"Mac, you realize that this is all speculation, right?" Riley said, not wanting to give up the matter so easily. "We have pretty solid evidence that Thornton's guilty," she reminded the blond. Mac nodded.

"I know," he conceded. "But-"

"I'm sorry," Jack interrupted. "I just...is no one else gonna ask who this dude is?" he asked, pointing to the stranger on the couch. Bozer and Riley looked at the blond expectantly as well, and Mac gave them a puzzled stare.

"This is Charles Conway," he explained as if that was supposed to answer all the questions they should have.

"Who is Charles Conway, and why is he here?" Bozer asked, encouraging his friend to continue his explanation.

"This is Thornton's guy," Mac replied. Bozer and Riley continued to look confused, but Jack had a look of understanding dawn on his face.

"So wait, you're the one that supposedly found evidence to prove that Thornton isn't Chrysalis?" Jack asked, unfolding his arms and pointing slightly at the man. Riley and Bozer's jaws hit the ground, but neither of them said anything. The man in the cowboy hat nodded, and Jack continued. "So what I want to know is how did you get this information?" Jack asked. "Did you somehow infiltrate the Organization and get them to convince to a secret microphone that they set Thornton up?"

Conway's eyebrow nearly disappeared off his forehead at Jack's question. "Nope...that's definitely _not_ what I did. That would be more up your alley as a spy, wouldn't it? I'm much more tech savvy than people savvy."

Jack inclined his head, silently agreeing with Conway's statement about it being more of a spy move. "So what did you do?" Jack asked again. Conway opened his mouth, but before he could answer, Riley cut in.

"I'm gonna save you some time, Charles. You're gonna need to not use regular tech-speak with Jack here," she explained. "You're gonna need to explain it to him like you would a child," she said, throwing a quick wink at the older man.

"You watch your attitude there, missy," Jack growled, completely in jest. He looked at Conway after that, motioning for him to begin his explanation.

"Alright, well let's see if I can explain it in a way you'll all understand," Conway said, looking around at the group. "I got on and I searched the deep web until I found conversations between two different people about setting up the bank account in Patricia's name. That's not enough proof to show she's innocent, but it's a start," he said. "Once I had that, I used algorithms of my own design to search the rest of the web and cross-match appearances of wherever Chrysalis seemed to appear as opposed to where Thornton was at that time."

"We had our techs run tests to try and find evidence of that," Riley replied, shaking her head. "There's no way they didn't find something along those lines."

"First, they don't have my algorithms," Conway stated. "Second, from what I hear from this young man, you're the best 'tech analyst' the Foundation has. Were you a part of that search team?" he asked, raising his eyes at the young woman.

Riley dipped her head a little. "No," she admitted.

"How hard do you think they really searched for information like that, if you already had the proof of the bank accounts?" he asked. Before any of them could answer, the man continued. "I'd also like to point out that there could be more than one mole," he said. "Even if they had searched for something hard enough and found something, I wouldn't be surprised if another mole hid or corrupted whatever information they found," he said. Everyone in the room had to give him that point; where there was one, there were usually more.

"So where's the information then?" Riley asked after a moment. Charles nodded towards the laptop in MacGyver's lap.

"Everything I've found is on that little hard drive," he said. "None of it is available via a wifi hack, either. You have to have physical access to this baby in order to get the information on her," he said proudly. Riley went over and sat next to MacGyver, and she glanced over the information on the screen. After a few seconds of watching her crane her neck to read the material on the screen, MacGyver simply lifted the computer off his lap and handed it over to the young woman so that she could read it easier.

A few minutes later, she lifted her eyes from the screen and stared at Conway. "You're saying you found all this?" she asked in mild disbelief.

"I did," the man in the cowboy hat confirmed.

"What sort of algorithm did you say you used?" she asked as she scrolled through the data once more.

"It was a collection algorithm of my own design," Conway explained. "I took the information that you found for Mr. MacGyver here that was used to convict Patricia, and I applied my algorithm to it. Before I had the evidence you folks had, all I did have were speculations and theories. Now that I've been able to apply my algorithms to all of the data combined, it should give us enough to at least get whoever is holding Thornton to take a second look at her case," he said.

"So you're a data miner?" Riley asked.

"That's one name for one of my many hats," Conway said, looking slightly smug.

"How did you and Thornton communicate?" Bozer asked. "We checked, she only had visitors from the CIA and Phoenix Foundation, and none of them were you."

Conway looked between the four of them, not sure if he wanted to tell them. "Look," MacGyver said, sensing the man's distrust. "We only want to find out what happened. We need to know the truth, and if it can help clear Thornton's name, we need to know anything and everything you can tell us," he insisted. Conway studied them for a moment more before finally nodding.

"We had a system," he explained. "It was how I used to communicate with her and others when I was doing time, and-"

"Wait, you were in prison?" Jack asked. "How long has Thornton known you?"

"Yes I was in prison, and we've known each other for several years, but I can either tell you how Thornton and I communicated, or I can expound on my imprisonment and my history with Thornton" Conway said, raising an eyebrow at Jack. "Which would you prefer?" When no one said anything else, the newcomer nodded his head and continued. "As a prisoner of the CIA, you are obviously allowed some privileges. One of those privileges is that you are allowed to have reading materials."

"So the book in her cell wasn't just for recreational reading," Mac said. It was a statement, not a question, and Conway nodded.

"We didn't have many interchanges, but when I found something, I sent her that book. I'm assuming that's when she reached and and requested to speak to you," he said, gesturing to the young man.

"So what was the code?" Jack asked. Conway raised his eyebrows at Jack again.

"What makes you think I'm gonna tell you?" he asked. "All you need to know is that the information we have collectively gathered should be enough to get your bosses to look at Thornton's case again," he said.

"I'm gonna call Sarah, tell her to get her team together and ready for a revisit to Patty's case," Jack stated as he pulled out his cell phone. He wandered into the next room so that the others could continue talking without the worry of interrupting his phone conversation.

The phone rang three times before Sarah's voicemail kicked in. Jack's mouth slanted, and he redialed the number. This time it rang twice, and just as he was expecting to have the voicemail answer again, he was pleasantly surprised when that wasn't the case.

"Jack," Sarah greeted. The older agent couldn't tell what emotion Sarah was feeling, but he was glad to hear that she didn't sound hostile or cranky. "Back from your mission then? Have you been updated on what's happened with Thornton?"

Jack immediately felt quiet alarms go off in his brain, but he ignored them for the moment. "Mission?" he asked. "What mission? And of course I'm up to date on what's happening with Thornton," he added.

"Look, I get it if you can't talk about the mission," Sarah assured her old friend. "I'm just glad you're aware of what's going on now," she said.

"Sarah, I'm serious, I don't know what mission you're talking about," Jack said. "And I've known what's been going on with Thornton since she broke out; Mac and I were there when they caught her again," he said, conveniently deciding to leave out the fact that he and Mac had been the ones who had led the CIA and Phoenix agents to Thornton. Something wasn't adding up with his conversation with Sarah.

"What are you talking about, you were there? When I talked with Phoenix agents, they said you and Mac had been sent out on an assignment," Sarah explained.

"Sarah, our last assignment was days ago," Jack said, getting a very bad feeling in his gut. "Just call our boss at the hospital," Jack said, feeling like a talk with Matty would clear everything up.

"Hospital?" Sarah asked. The longer their conversation went on, the less and less comfortable Jack became.

"Yeah, hospital," Jack repeated, finally accepting his gut feeling that something was wrong.

"I got word from your people at the Phoenix that said they had caught Thornton and they were taking her back to a holding cell at the Phoenix," she explained. "They were going to debrief her and do some interrogation before taking her back to the CIA supermax," she said.

"No," Jack said slowly. "She...I mean, it's a long story, but basically the gist of it is that she didn't break out voluntarily; she was abducted, and when she got away from her abductors, they managed to shoot her. It got her kidney, and she's spent the last several hours recovering from emergency surgery in the Phoenix medical center," Jack explained.

"Jack, that's not what I was told by your people over the phone," Sarah said.

"I know, and I get the feeling that both of us have been led on," Jack said.

"What's that supposed to mean?" Sarah asked, not liking how this conversation had turned out.

"I'll have to tell you later," Jack said. "Right now I've got to get over to the hospital."

 _0-0-0_

While Jack walked into the next room, MacGyver looked at Riley, remembering what else Thornton had told him to look up. "Hey, did you ever pull those files on Berkhoff?" he asked. Riley nodded, pulling out her own computer and putting in the password before she handed it over to the blond.

"Everything is in that folder in the top left corner," she instructed. Mac double clicked on the manila envelope icon and pulled up everything that had been filed about the botched exfil.

He read over it once, but something wasn't sitting right with him, so he read over it again. "Riley, did you read through this?" he asked once he had finished his second read-through.

"No, I skimmed it, but we kinda had to run after you and Jack went AWOL," she explained. "From the few lines I did read, I didn't really see anything out of the ordinary," she added. Mac furrowed his eyebrows and went back through and read it one more time, and finally something clicked. He looked up with a wild expression on his face.

"I got it," he said, standing up in excitement. Bozer, Riley, and Conway all stared at him with expectant looks, but Mac simply stood there, staring at the computer in his hands.

"Okay, are you gonna tell us?" Bozer prompted, knowing how his roommate could get once he got excited about something. He had the tendency to think people immediately knew what he was thinking, and sometimes he had to be reminded that people hadn't developed the ability to read minds yet.

MacGyver was about to respond, but Jack walked out of the room he had taken his call to. Mac looked over at his partner. "Jack, Berkhoff's body was-Jack?" Mac said, stopping his explanation short when he saw the grim look on his partner's face. The blond immediately knew something was wrong, and he got a sinking feeling in his gut. "Jack?" he asked warily. "What's wrong?"

"We've been played," Jack said. "We need to get over to the hospital. Now."

 _ **Dun dun dun...What's goin' on?!**_

 _ **Lol okay so last night, I showed my mom the season finale of MacGyver, and she can't handle a lot of stress without something funny afterwards, so after that, we watched Monster Trucks, and she LOVED it. Unashamed promo for Monster Trucks because it's a good, pure, clean and funny movie, albeit a little cheesy. But hey. Who doesn't love cheese, am I right? ;) I mean, you all read my stories, so you at least have a decent tolerance for it anyway XD Anyways...go watch Monster Trucks. Please ;)**_

 ** _Okay last night I had a dream all about me, Murdoc, and MacGyver, and I think Harry Potter came in a little bit, but it was such an exciting dream and I didn't want to wake up... :( But at least I remember most of it, and the whump that took place in it XD I sound so demented. Anyway, I just had to get that out there!_**

 ** _Lemme know what you think of the story! Is it okay and easy to follow? This is the part where I think I was having the most trouble with all my jumbled thoughts, so let me know if it makes sense or not!_**


	6. Chapter 6

_**Hello friends! Guess what! New chapter! Also, it's the last week of classes, and I could just cry for joy!**_

 _ **Longer AN bottom :)**_

Mac looked at his phone angrily. "She's still not picking up," he informed his partner, who was driving like a madman through the streets of LA.

"We're almost there," Jack tried assuring the younger man. "Look, I'll drop you off so you can go find Matty and let her know what's going on while I park the car," he said. Mac looked out the window and felt the pressure in his stomach release slightly as he saw the hospital getting closer and closer.

Jack screeched to a halt outside the entrance, but Mac didn't even wait for the car to come to a complete stop before his seatbelt was off and his door was open. He slammed the door shut and sprinted into the hospital while Jack drove towards the parking garage.

MacGyver rushed through the hospital, ignoring the guards yelling for him to stop. He ducked and dodged doctors and nurses, shouting apologies as he made his way through the hallways. He finally saw his boss talking to one of the doctors, and he made his way towards her.

"Matty," he called out. The director of the Phoenix Foundation looked over at him, her eyes going wide in surprise, then narrowing almost instantly.

"I thought you were supposed to be staying at home, MacGyver," she snapped, walking towards him.

"I know, but we have reason to believe Thornton's in danger," he said, panting slightly as he came to a stop. "I need to talk to her," he said. Marty shook her head.

"Even if I was willing to let you in to talk to her after you disobeyed my direct order to stay home, you can't. The CIA came and insisted that she would be taken care of at their medical facility, so she was released into their custody," the woman explained. "It's not what I wanted to have happen, but since she is being investigated by the CIA primarily, they technically have jurisdiction if they want her." Mac's eyes widened.

"How long ago did they leave?" he asked urgently. Matty looked confused as she answered.

"A little less than ten minutes ago," she replied, her tone clearly indicating she wanted the blond to tell her what was going on. MacGyver turned around and pulled out his phone as he made his way down the hallway, ignoring the daggers being glared at his back by Matty.

"Riley," he said when the hacker answered. "Thornton's been taken," he explained. "I need you to hack into the hospital security system and find the vehicle that took her, see if you can track it," he said.

"I'm on it," Riley replied.

"Mac," Matty called out frustratedly. The blond turned and looked at his boss. Her expectant look was not lost on the blond, but he knew he didn't have time to stop and explain.

"Bozer'll be here in a few minutes," Mac said. "He'll explain everything then!"

Matty watched the young man take off down the hallway, her temper flaring wildly. She didn't show it though; she had to keep a calm and cool demeanor. She began to walk down the hallway, intending to pull out her phone and call MacGyver, but one of the doctors caught up to her, distracting her for a moment as they went over the medical files on Thornton. Matty knew she needed to go after MacGyver, but the doctor wouldn't leave her alone until she had signed the different release forms.

As promised, a few minutes after MacGyver ran out of her sight, the elevator doors at the end of the hallway dinged open, revealing Bozer standing in the lift. Matty heard the doors open and saw the newest Phoenix agent standing there, and she quickly handed the doctor his files and forms before turning and stalking towards the young man.

"Bozer, what on earth is going on?" Matty asked, sounding more cross than Bozer had heard her since...well, ever. "Mac came running in here said something about Thornton being in danger before running away once I told him she had been taken back into CIA custody," Matty snapped. "I gave him a bit of leeway by giving him the chance to talk to Thornton earlier, but I was serious when I said he was supposed to stay at his hou-"

"Matty," Bozer interrupted. Matty stopped mid-sentence, giving Bozer a look that told him he was on very thin ice. "Respectfully, ma'am, Mac didn't really have a choice," he stated. "We have reason to believe that those men who took Thornton weren't with the CIA," Bozer explained. "We also found evidence that proves Thornton may not be Chrysalis after all," he added.

"And what gives you that idea?" Matty asked. Bozer looked a little uncomfortable as he glanced around.

"Well, about the evidence, I'd love to explain it, but it's a ton of tech-talk, and while I'm better than Jack is at explaining stuff like that, I'm nowhere near as good as Riley, and I think I'd just end up convincing you that Thornton's guilty even more. I'd much rather wait for Riley," he said. "As for Thornton being in danger, Jack called Sarah Adler, one of his old friends from the CIA-,"

"I know who Sarah is," Matty interjected. Bozer looked confused for a minute before remembering that Matty and Jack had worked in the CIA together, so it made sense that she and Sarah knew each other.

"Right," he said, shaking his head slightly. "Anyways, Sarah said that she talked to Phoenix agents who told her that the Foundation had requested to take custody of Thornton," he said.

"That's not true," Matty said. "I just talked with agents from the CIA, and they-" Matty paused as she realized that they had indeed been duped.

"Matty," Bozer said as he saw his boss's look of understanding come over her face. "Mac and Jack are going after the people who took Thornton, and I think they could use some backup," he said. Matty nodded, and she pulled out her cell phone.

"This is Director Webber," she said once the person on the other end picked up. "I need someone to find the location of MacGyver and Dalton, and I need backup to that location ASAP," she instructed. She hung up and marched down the hallway, Bozer tailing behind her.

 _0-0-0_

MacGyver heard Matty start to say something else in a very strict voice as he sprinted down the hallway, but he knew he couldn't spare the time to listen to her lecture. He tuned her out and hit another contact number on his phone as he turned the corner, heading for the stairwell. He had to dodge several nurses, who gave small cries of alarm, but he simply shouted his apologies as he pushed the door open. Finally, Jack answered his phone.

"Jack, she's already gone," Mac said as he ran down the stairs, knowing he could get down on his own faster than waiting for the elevator.

"What? When?" Jack asked.

"Ten minutes ago," Mac replied, panting as he jumped down two steps at a time. He knew time was of the utmost importance right now. "I need you to meet me at the front of the hospital again," he said.

"Thirty seconds out," Jack promised. Mac heard the car accelerate, and heard the squealing of the tires as he assumed Jack rounded one of the corners in the large parking garage. Mac got to the front right as Jack pulled up, and Mac yanked the passenger side door open. Jack shot out of the hospital lot as soon as he saw the kid's door close, and while he was driving, Mac got Riley back on the phone.

"Riley, tell me you got something," he implored as she picked up.

"I did," she confirmed. "She was taken out to a black sedan, and I got a hit on the plates. The car's registered to a dummy corporation, but the nice thing about this model of sedan is that it's all electronic, meaning I can track it. They just took a left on Paradise Falls Road, so if you cut across-"

"Cut across Bridgerland, we should be able to catch them," Mac finished her sentence for her, a spark of hope igniting in his chest. "Jack?"

"On it," Jack said, yanking the wheel hard to the left, throwing Mac against the window slightly.

"Okay, once you're on Bridgerland, you're going to take a right when you see Oakridge Street," Riley instructed, now on speaker phone so that MacGyver didn't have to keep relaying the information. Jack sped down the street they were on until he spotted the sign for Oakridge, and he turned the corner, barely avoiding going up on the curb. He received several angry yells of anger from pedestrians on the sidewalk, but Jack ignored them.

"Guys, they should just be passing you," Riley suddenly said. MacGyver and Jack looked out the windshield and they did indeed see a black sedan drive past them, driving at a decent clip. They weren't going fast enough for most cops to pull them over, but they were going quite a bit faster than normal traffic. Jack made another left-hand turn, merging into traffic right behind them, cutting off several cars in the process and causing those people to honk at them and throw out several rude words and gestures.

A few seconds after they pulled behind the vehicle, the sedan suddenly sped up and took a right-hand turn, depositing them on a narrow alley street. Jack turned the corner to keep following them, but he slammed on his brakes as he and Mac saw the car had pulled to a stop about halfway up the alley.

Jack threw the car into park, and he and MacGyver cautiously got out of their car, keeping behind their doors as a slight shield. MacGyver looked behind them, seeing the light traffic continue to pass by. They were only a few feet into the alley; Jack had wanted to keep a decent distance between them and the other car, just in case. As the two agents watched, the doors of the other car were flung open, and a man got out from each side, four men in total. They all had scratches on their faces, showing Thornton had put up quite a fight, even while restrained. Even in the serious situation, Mac couldn't help the smug, proud feeling for Thornton that spread throughout his body. That woman never stopped fighting, and it was something Mac had always respected her for.

All four fake CIA agents trained their guns on the two Phoenix agents; Jack pulled out his own gun, while Mac put his hands slowly in the air, showing that he was unarmed.

"Put your gun down!" one of the men ordered sharply. Jack shook his head slightly.

"No can do, compadre," he called back. "Let me talk to Patty," he insisted. While the older man was talking, Mac's eyes were darting around, trying to think of a way to help them. He spotted a fire hose lying on the ground a few feet away, and his brain went into overdrive.

"No can do, compadre," parroted the first man condescendingly.

"Oh yeah, real mature," Jack drawled. The other man smirked and shrugged his shoulder slightly.

"Get back in your car and drive away," the man ordered. "This doesn't concern you."

"See, that's where you're wrong," Jack replied. "That's our friend you've got in the back of your car, and we don't like what you've got planned for her," he explained.

"I dunno what it is you think we have planned for her," the man called back. "We just wanna talk!"

"Uh huh, and by 'talk' I'm pretty sure you mean 'put a bullet in her brain,'" Jack quipped.

"We're not going to kill her," another man insisted. "She's no use to us dead!"

"No use?" Jack asked, glancing at his partner in confusion. Mac shrugged, and Jack faced the men again. "Still, pretty sure once you've gotten whatever you need from her, she's gonna be pretty expendable," Jack reasoned. "She'll have become a loose end, and we all know how people feel about loose ends."

"Well, even if you tried to get her from us, I think you're a little confused," the other man said. "You'd never be able to get to her. There're four of us, and only two of you," he reminded Jack.

"That's true," Jack conceded. "But you guys are also confused," he added, drawing chuckles from the men.

"And why is that?"

"You guys may outnumber us, but we've got a secret weapon," Jack said, giving his partner a sidelong glance. Mac gave a small nod, and Jack continued. "We've got MacGyver on our side," he stated. As soon as he said that, Mac dove for the long white hose, grabbing as much as he could and running for the mouth of the alley, where he remembered seeing a fire hydrant.

"Mac, this was not what I was thinking!" Jack yelled after his partner. "I sure hope you've got a quick solution!" Jack added loudly as the bullets began flying. Mac heard Jack grunt, and looked over to see that the men posing as CIA agents had shot at Jack's car door, and the driver's window was shattered. The older Phoenix agent had crouched down though, and thankfully didn't seem to be injured. Mac ducked and covered his head as several bullets pinged off the bricks above him, trying to make himself as small a target as possible.

Mac exited the alley and found a fire hydrant barely five feet away. He quickly attached the hose to the hydrant, but he suddenly realized he didn't have anything to turn the nut on hydrant to release the water. He glanced down frantically, but before he could really look for something, Jack hurtled around the corner of the alley, pressing himself against the wall and staring at Mac.

"Mac, I was kinda hoping for something a little more immediate," Jack admitted loudly over the sound of gunfire.

"Sorry I was trying not to get shot instead of building a way for us to get Thornton," Mac quipped at his partner.

Jack fired off a few more shots before he and Mac heard a clicking coming from the gun. "I'm out," Jack informed his friend apologetically, sticking his gun back into the back of his pants.

"Wait, gimme that," Mac said, holding out his hand.

"My gu-whaddya want my gun for, dude?" Jack asked as he pulled it out and handed it to his partner. Mac didn't answer as he ejected the empty magazine clip. Once the mag was out, he stuck the butt of the gun over the nut; the gun was a little bigger than the bolt, but once he began turning it, it caught on one of the hexagonal sides.

"Hold this," Mac grunted as he dumped the water hose in Jack's lap.

"What the-"

"Just aim it!" Mac instructed as he turned the gun quickly, loosening the bolt and releasing the water.

Jack's eyes widened as the hose filled with water and he quickly turned the corner and aimed it towards the men advancing on them. The fake CIA agents sputtered and dropped their guns as the torrent of water barreled into them with enough force that they were forced back towards their car. There were a few small holes in the hose, which didn't actually surprise Mac, seeing as how he found it abandoned on the road in an alley, but it was doing the trick. After a few moments of spraying the men, Mac shut the water off and he and Jack ran from behind the corner while the men were still distracted, preparing to fight hand-to-hand.

MacGyver ran and leapt on the back of one man, knocking his gun to the ground in the process. Mac kicked the weapon out of the reach of its owner, but he had to kick the man's arm when he reached out to try and grab the weapon anyway. The two of them struggled for a minute; the man got a shot at Mac's face with his elbow, causing the blond to reel back slightly, his forehead pulsing in beat with his heart. The man got to his feet and lunged for Mac, but the blond quickly sidestepped the charging man, digging his own elbow into the back of the man's neck. When the man cried out in pain, Mac took advantage of his distractedness and delivered a final punch to his face, sending his opponent to the ground. Mac cradled his fist for a second, shaking it out in pain, but he had to forget about the pain in his wrist as he was jumped from behind. He was thrown to the ground, the second man's weight on top of him preventing him from getting back up.

"You should have left when you were given the chance," the man sneered as he pushed Mac's head down onto the ground and placed his gun against the side of Mac's temple. The blond bucked a bit under the man to try and dislodge him, but before he could put up much of a fight, there was another voice above the two of them.

"And you should have given up when _you_ were given the chance," Jack said. There was a _thud,_ and then the weight was suddenly gone from Mac's back. The young man rolled over seeing Jack standing above him and accepting his partner's outstretched hand.

"I had him," Mac said, though there was no fight or anger at all behind his words. Jack smirked at his young partner as he helped him to his feet.

"Uh huh, sure you did," he replied sarcastically. Mac shook his head with a small smile and the two of them hurried over to the large suburban. Mac pulled one of the back doors open, revealing Thornton tied to the back seat with a gag in her mouth. Her face was ashen, and Mac could only assume it was because of the injury in her side, but he figured they would deal with that injury later as he climbed into the back seat and pulled out his pocket knife, cutting through the zip ties around her wrists. She took the gag out of her mouth, giving it a slightly disgusted look as she discarded it on the ground.

"Just...stay there," Jack said, motioning for his ex-boss to stay where she was so that she didn't exacerbate her injury even more. "It'll probably be easier for us to get you outta here in this car rather than tryin' to get you over to our car," he reasoned.

Thornton merely nodded in response; she was loathe to admit it, but she was drained, and her side was killing her. The men hadn't exactly been gentle while getting her into the car, and once they realized they were being tailed, they had taken corners rather sharply which caused more pain for Thornton than she was already experiencing.

Jack and Mac climbed out of the sedan, but before they could get to the front of the car they heard brakes screeching to a halt behind them. The two of them turned and looked, and they saw Phoenix agents pouring out of almost half a dozen cars that had parked on the street behind Mac and Jack's now-bullet-riddled car. The newly arrived agents moved forward, and after making sure the men on the ground were restrained properly, they moved towards MacGyver and Jack. At the front of the group was Sarah Adler, her gun pulled out and held in front of her.

"Wait," Mac said as the Phoenix agents moved towards Thornton to take their former boss into custody. "She's innocent," he insisted. Sarah gave the blond a sympathetic look, but didn't make a move to stop the agents from grabbing Patricia's arm. Before they could get very far though, another voice cut in and stopped everyone in their tracks.

"Hold it," Matty said sternly. Everyone turned to look at her as she walked towards the vehicle where Thornton was sitting. Mac stared at his current boss as she walked over to them, a look of slight apprehension on his face. "For the foreseeable future, Patricia Thornton will be staying in the custody of the Phoenix Foundation, with me and my team," Matty stated as she neared them. Matty stared at Sarah for a second. "I trust that that's alright with everyone?" she asked, though it was phrased in such a way that no one felt confident enough to argue with her. Sarah nodded.

"I understand," she said. She didn't look especially happy about it, but she understood why the new director of the Phoenix Foundation was only trusting a small team, which would no doubt contain MacGyver and Jack; they had all been taken in by the members of The Organization, and had almost lost Thornton as a result of it. Matty knew her agents better than the CIA did, seeing as there were a much smaller number of Phoenix agents than there were CIA agents, and therefore easier to keep track of who was and wasn't actually employed with them. Sarah looked at Jack and Matty.

"I'd like to stop by the Foundation later to talk to Thornton though," Sarah requested. Matty nodded.

"That's fine," she agreed. "Just as long as she doesn't leave Phoenix HQ, and me or one of my team members is there as well," she added. Sarah nodded in agreement.

"I think that's something I can agree to," she said. Jack looked over at the injured woman who was being surrounded by Phoenix agents to be escorted to another car. When the conversation lulled between Matty and Sarah, he jumped in and inserted a question for Thornton.

"Patty," Jack said as the ex-director was led to another vehicle. "These guys said you'd be of no use to them dead. Do you know what they were talking about? What did they want?"

Thornton looked at MacGyver, and he realized he knew the answer even before she said it.

"They wanted me to give them the location of Agent Berkhoff."

 _ **Uuuuhhhh...whaaaat?**_

 _ **Okay, so I got the hose thing from an old episode of MacGyver, I think it was "Tough Boys," but I tweaked it a little. Also, I don't know if Riley can track the car that way, but we're gonna pretend she can XD**_

 _ **So, thoughts? Let me know what you think? :D**_


	7. Chapter 7

_**I don't own MacGyver or Harry Potter... XD**_

 _ **Also, not quite sure about how I feel about Matty & Patty once the team leaves...to me it kinda seemed OOC, but I felt like they needed to talk? I dunno...**_

"Okay, I'm confused," Matty said as the small team gathered around the Phoenix bed Thornton was laying on. "Agent Berkhoff is alive?"

"Agent Berkhoff, the same agent who was shot down during exfil in Syria, is still out there, and you didn't tell anyone?" Jack asked as well, staring at Patricia with slightly narrowed eyes.

"I couldn't tell anyone," Thornton insisted. Her old team, along with Matty, stared at the woman with skepticism. "Look," Thornton said. "Berkhoff stumbled onto information regarding the mole during his mission. He contacted me, and we both knew that whoever the mole was knew he had found something. We also knew that there was no way they were going to let him live. So we didn't actually put him on the chopper," Thornton explained.

"There was a rumour that the Syrian terrorist cell he was after had stolen his body, and that's why it was never recovered," Jack said, realization dawning on his face.

"There were never any Syrian terrorists," Thornton said, shaking her head slightly. "Or, there were, but they were nothing to be worried about. There were only a small number of them, and they were easily subdued."

"This is some freaky Peter Petergrew stuff right here," Jack commented.

"Um, I think you're thinking Peter Pettigrew, if you're referring to the character from Harry Potter," Mac corrected.

"Meh," Jack replied, waving off his partner's correction.

"Anyways," Matty interrupted, giving Jack the stink-eye. "Does Berkhoff have the name of the mole?" she asked. Thornton shook her head again.

"No," she replied. "If he did, don't you think I would have called him in the minute I was arrested?"

"Fair point," Matty conceded. "So what information did he find that put him in the crosshairs of The Organization?"

"He was the first one, at least to my knowledge, to find out that there was a mole; he brought it to my attention, and we silently started looking into everyone once he was safe. Even with our best intentions to stay quiet though, I think we made more noise than we intended, and The Organization found out about our investigation. That's when they started putting together the evidence to frame me. The Organization is just wanting to get rid of all loose ends," she said. "I'm assuming they were going to interrogate me until I told them where Berkhoff was, and if I did, they would probably have kept me alive to make sure I'd given them the right information, gone to get him, brought him back, and killed both of us at the same time," she explained.

"So...where is Berkhoff?" Riley asked after a minute. Thornton looked at the people surrounding her, knowing she could trust them completely.

"Canon City, Colorado," she finally replied. "I'll give you the new identity he was given, but I need you to promise me that you'll bring him back alive," she insisted.

"'Course, Patty," Jack assured her.

"While we're at it, I thought you guys said you found evidence proving Thornton's innocence?" Matty asked.

"Yeah, but most of it is with Thornton's-"

"Thornton's guy," Matty finished, sounding slightly exasperated. "Wait, most of it?" she asked as she realized what Mac had said.

"Well," Riley replied. "I did a bit of digging, and while I don't have as much as Conway, I was able to find something."

"It's all just a bunch of techno hooey mumbo-jumbo," Jack supplied helpfully as Riley pulled out her tablet and handed it to her boss. Riley glared at the older man.

"It's actually a little more sophisticated than that," she said sarcastically, tapping a few things on the screen. "I went back and was able to find the conversation that Nikki had with Chrysalis. Y'know, back in the hotel."

"What about it?" Matty asked.

"I read through the messages and didn't find anything useful there; it was basically just what Mac said it was. Nikki telling Chrysalis that she had copies of what had been in the lock box and was willing to sell them. Nothing helpful," she said. "But when I started looking at where the messages had been sent from, I found that there was a scrambler code for the IP address, mixing up the IP numbers and making it difficult to track down where Chrysalis was actually messaging from."

"Which was?"

"After applying an algorithm I've been working on to descramble the numbers and put them back into place, it looks like it was coming from a location somewhere in La Jolla, which Thornton was nowhere near that night," Riley explained. "It's not enough to prove she's innocent, but I'm thinking that this, plus the evidence Thornton's guy gathered may be enough to have Oversight take another look at everything."

Matty nodded thoughtfully as she looked through the information Riley had just handed her.

"Where _is_ Conway?" Thornton asked as she realized that she hadn't seen him anywhere, even though she was assuming Mac had gotten ahold of him.

"When we left to get you, he was at my house," Mac replied, looking to Riley and Bozer for a more helpful answer.

"Yeah, but after you and Jack ran out the door, he kinda up and left, saying it was safer for him if we didn't stick with him," Bozer added. "He didn't want the only copy of the evidence he'd gathered for Thornton to fall into the wrong hands," he explained as everyone looked at him in confusion.

"Well I still have yet to meet this 'guy' or see the supposed evidence he's gathered, so for now, Patricia, I'm sorry. I'm going to have to keep you in custody until I can see the evidence that Blondie and Jack say they've found," she said, actually sounding apologetic.

"I understand," Thornton said tiredly. "Mac, do you still have Conway's number?"

"Yeah," he said, pulling the crumpled piece of paper out of his back pocket. "Want me to call him?"

Thornton nodded. "He won't want to come here though," she added. "Someone is going to need to go somewhere to meet him and get the information," she explained.

"Riley, you and Bozer go get the information from Thornton's man," Matty instructed. "Mac, Jack, you two are going to Colorado to find Agent Berkhoff and bring him back here," she continued.

"Yes ma'am," everyone replied simultaneously. MacGyver handed Riley the piece of paper with Conway's number on it, then he and Jack walked out the door, followed soon after by Riley and Bozer. Matty walked over and sat in one of the chairs next to the bed Thornton was on.

"Matilda Webber," Thornton said in a contemplative voice after a few moments of silence. Matty looked at Thornton, quirking her eyebrow up a little.

"Patricia Thornton," she replied in the same tone.

"You've got quite the reputation among government agencies," Thornton commented.

"I could say the same about you," Matty said. "Before you were arrested, I mean," she clarified. Thornton's mouth twitched upwards in a ghost of a smile as she thought about the rumors that must be flying around about her now.

"I hope you understand that this is all protocol?" Matty asked after a few more moments, gesturing to the restraints securing Thornton to the bed.

"I understand," Thornton assured Matty. "I'd do the same thing if our roles were reversed." Another few moments of slightly awkward silence passed before Patricia spoke again. "I'm glad you're the one who replaced me," she admitted. "You've got an amazing background experience, and the team seems to be doing just fine."

"It's been quite the journey," Matty agreed. "And while I don't agree with everything that Mac or Jack do, they are quite honestly the best team the Phoenix has; my guess is they wouldn't have gotten there without you."

Thornton didn't say anything to that; she simply looked out the door where her-where Matty's team had disappeared through. Matty stared at the brunette for a minute, a thoughtful look on her face. She couldn't help but think to herself that if Thornton was the mole, she did an amazing job of pretending like she actually cared about her team. Matty had only heard about Thornton through reputation before, but being with her now made the new Phoenix director wonder if Thornton really could have pulled off caring for her team as much as she seemed to. Matty understood that Patricia Thornton was one of the best spies in the country, but it would have been hard for even her to pull off the real emotion she was showing on her face at the moment.

Matty didn't say anything else. She simply let the silence grow louder and louder while they waited for any word from any of the team. Finally, Thornton's eyes drifted shut; Matty had had the doctors give her more painkillers, and it seemed like they finally kicked in. After Thornton drifted off to sleep, Matty simply continued to sit there, wondering what was going to happen. She wasn't planning on leaving Thornton alone anytime soon. Even if she really was the mole, she deserved to be in prison, not dead. The more and more Matty thought about it though, the more she began to think MacGyver was right, and that they had all been played.

 _0-0-0_

MacGyver and Jack settled down in the plane's seats, and as soon as they felt the plane take off, they both relaxed slightly. Mac's eyes began drooping, and while he knew that he and Jack should probably talk about what their plan was once they touched down in Colorado, he had been up for over thirty-six hours, with maybe thirty minutes of sleep throughout the entire time. He was exhausted, and he could tell Jack was too. Soon, Mac's eyes shut all the way, and he drifted off to sleep.

 _0-0-0_

"Mac? Mac!" a distorted voice sounded above him. Mac opened his eyes swiftly, sitting up and staring around him with a slightly confused expression, until he remembered where he was. "Sorry to wake ya up, but I figured we should probably go over our game plan," Jack said as he looked at his partner apologetically. He knew how draining the last few days had been for his partner, both emotionally and physically.

"How long was I out?" Mac asked, moving his tongue around his mouth to get the taste of sleep out.

"A little more than two hours," Jack replied, checking his watch. "We've only got about fifteen more minutes before we land," he added. "You got our dude's information?" he asked. Matty had instructed them not to use Berkhoff's name at all, even in front of other Phoenix Agents, just because they didn't know if anyone else was a mole and working for The Organization.

"Yeah," Mac said, rubbing the last bit of sleep out of his eyes and sitting up further. He reached into his pocket and pulled out a slip of paper, on which Thornton had written the alias and address for Berkhoff. He handed it over to Jack, who examined the writing on the paper.

"Peter Winkler," he read quietly, looking around to make sure he and his partner were alone. "So what're we gonna do when we get there?" he asked. "Walk right up to him and say 'Hey, listen, we think your life's in danger, so we need you to come back with us to the Phoenix Foundation'?"

"First of all, he won't know what the Phoenix Foundation is," Mac pointed out. "Not unless Thornton told him about the rebuild. He...disappeared while we were still DXS," he reminded his partner. "But we do need to make him realize that his life really is in danger and get him back on the plane; once he's safe, we can do a bit more explaining."

"Are you saying we kidnap him?" Jack asked, raising an eyebrow at his partner.

"No," Mac replied, shaking his head with a chuckle. "We want him to trust us, remember? Kidnapping him won't really help with that."

"It kinda worked with Anja," Jack pointed out, referring to the first time they met their Russian friend.

"No, she was terrified of you," Mac argued. "It was only after I told you to put her down that she started to trust us!"

"So let's do the same thing with Berkhoff!" Jack proposed, only partially kidding. Mac rolled his eyes at his partner, making it clear that they were _NOT_ going to fake kidnap Berkhoff just to get him to trust them.

"I think your logic is a little twisted," Mac snarked at his partner.

"Your...face is...twisted," Jack shot back, struggling to come up with a good retort. Mac raised his eyebrows at his partner in amusement. "Okay then," Jack said, throwing up his hands in mock exasperation. "Use that big brain of yours to come up with another genius idea!"

"Actually, I think your idea of walking up to him and telling him straight up that he's in danger is probably our best approach," Mac said with a shrug. "It's honest, and honesty is probably the best thing we have to work with right now."

Jack perked up a little, and he looked at Mac. "Are you saying that my idea is the best one?" he asked.

"That's what I just said, isn't it? Besides, out of the two ideas that we've had, which have both been yours, the other idea was that we kidnap him. Talking seems like the more logical solution out of the two ideas," Mac answered drily.

"Yeah, but I wanna hear you actually say it," Jack pressed.

"Not sayin' what's already been said, Jack," MacGyver said, shrugging his shoulders and smirking at his partner.

"Dude," Jack griped.

"Oh look, we're starting the descent," Mac said, steering the conversation in a different direction. "It looks like his address is only about thirty minutes away from where we're landing," Mac added, pulling up the map on his phone. Jack leaned over and looked at the route on the map, nodding as he looked it over.

A few minutes later, the plane touched down, and Mac and Jack stood up, waiting for the plane to taxi to a stop. Once the side door was opened, the two of them hurried off the plane. They spotted a car waiting for them at the end of the airstrip, and they quickly made their way over. Jack grabbed the keys from the top of the visor once he and Mac were both in the car, and he turned the car on. He glanced over at the map Mac still had pulled up on his phone before driving onto the streets of Colorado. They merged into traffic, neither of them noticing the inconspicuous blue Honda that pulled into traffic several cars behind them.

 _ **Ok! Guesses? Thoughts? Yes, I'm very much taking creative license with a lot of technological things in this story, I know XD**_

 _ **So did you guys think Matty & Patty were OOC? Probably? **_

_**Lemme know what you guys think!**_


	8. Chapter 8

**_Hello! I'm glad that you're all enjoying the story so much! I am a little sorry about the cliffhangers...I hope you all enjoy chapter 8!_**

Riley and Bozer hurried into the room where Thornton and Matty were sitting. The two older women stared at the two younger agents, confused as to why the two agents seemed so frazzled.

"Did you get it?" Matty asked, looking expectantly at the bag that held Riley's laptops.

"Yeah, I got it," the young hacker replied. "He didn't want to let it go, but he let me take it once I told him we'd owe him," she explained slightly hesitantly, unsure of how Matty would react upon hearing that they were now in debt to Charles Conway. Matty didn't look especially happy about it, but she didn't say anything as she accepted the laptop Riley handed her. Matty's eyes scanned over the files before her, taking in all the information available.

"How did your man find this stuff?" Matty asked as she looked over at Thornton. "We had our techs, as well as CIA techs run tests to try and find any evidence like this."

"He's good at finding things people don't want found," Thornton replied simply.

"Plus," Bozer added. "We think there may be more than one person belonging to The Organization working both here and in the CIA."

"We've been worried about that ever since we found out there _was_ a mole," Matty agreed.

"We think they may be sabotaging the work that our tech teams try to get done, burying any real leads that we get on The Organization," Riley explained. Matty nodded, acknowledging the fact that it was a very real worry.

"I mean, this is pretty incriminating stuff," Matty said as she continued to look through the evidence. "There are chats here from different users talking about setting Thornton up to take the fall. They don't mention you by name, but they talk about the scapegoat as 'The Director,'" Matty said, addressing Thornton as she scrolled through the chats. "How did he find this?" she asked again.

"He's a data miner," Riley supplied. "It's his job to go through and find online data people thought were gone. He had to go deep; The Organization has some amazing tech people working for them that did a good job of covering their tracks."

"And to be fair," Bozer said. "I'm wondering how hard our people actually looked; don't take that the wrong way, but I mean, we had Thornton. What more searching did we need to do? We had the bank accounts in Thornton's name, she didn't try to convince us she was innocent, and I'm just wondering how hard the evidence was really searched for and looked through."

Matty looked at Bozer, not sure if she should be upset at what he was insinuating, but Riley interrupted before she could make up her mind.

"Also," Riley interrupted, urgency apparent in her voice. "Do you remember Olivia Prior?" she asked. Matty looked at the hacker in confusion.

"The woman from Amsterdam?" she clarified. "Of course I remember her. What does she have to do with the evidence Thornton's man gathered?"

"A lot," Bozer assured his boss as Riley pulled up a file on the laptop Conway had given her. Thornton was watching all of this go down with, for the first time in a long time, what looked like a spark of hope in her eyes.

"He was able to do was reconstruct the phone call Olivia received," Riley explained as she pulled up the file.

"The one where she was told to drop the bomb as soon as she saw someone following her?" Matty asked.

"No," Riley said, shaking her head. "The original blackmail call."

"How was he able to do that?" Matty asked, sounding skeptical. "That call was months ago."

"When Chrysalis called Prior, she used what's called VOIP, or 'Voice over Internet Protocol,'" Riley explained. "What that means is that instead of using cellular data and phone lines to talk, the call uses the internet. It makes it harder for people to listen in on or track while the call is taking place, especially since it's relatively easy to bounce a VOIP call signal all over, so no one can pin down your location while you're on the phone but you know the saying: Nothing is ever really deleted from the internet." With that statement, Riley hit the play button on her computer and watched Matty and Thornton's reactions.

 _"Hello?"_

 _"Olivia Prior?"_

 _"Yes, who is this?"_

 _"You don't need to know that."_ Thornton's eyes widened as she recognized the voice and she looked at Riley, who was staring back at her with a grim face.

 _"What are you talking about? Of course I need to know! Why are you calling me? And how did you get this number? This is my private cell phone, and-"_

 _"All you need to know is that you are going to do exactly what I say, otherwise the whole world finds out about your little affair."_

 _"I don't know what you're talking ab-who is this?!"_

 _"You can call me Pop. But who I am isn't important. It's the information I have on you that should be your main concern."_

 _"What is it you think you have?"_

 _"I have pictures here, Mrs. Prior. Pictures that I'm sure you don't want to get out."_

 _"I don't believe you."_

 _"No? I'd check your most recent text messages before you make a final decision about whether you believe me or not."_

There were a few moments of silence, then Olivia came back on the line. _"What do you want?"_

The phone conversation continued, but the small group didn't really pay attention as Matty began talking. "Well, I can tell that's not Thornton's voice, and it sounds familiar, but-"

"You probably wouldn't recognize her voice right off the bat," Riley assured her boss. "You've only met her once or twice," she added.

Matty listened a little harder as "Pop" instructed Prior on what she was going to do, and suddenly she recognized the voice on the other end of the line, the voice threatening to release the blackmail photos of Prior. Her eyes also went wide, and she pulled out her phone immediately. She hit Mac's number and held the phone up to her ear, tapping her foot.

"Come on Mac," she muttered. "Pick up!"

0-0-0

"Okay, this is it," Mac said as Jack rolled up to a house on the outskirts of a neighborhood. It was a small house, but if only one person were living there it looked like it could actually be quite roomy.

"Should we go over the plan again?" Jack asked as he looked at the house.

"Jack, what is there to go over?" Mac asked, slightly exasperated. "We go up, knock on the front door, and when he answers, we explain what's going on."

"I know, but I just really want you to say that my idea was the best one," Jack admitted with a sheepish grin. Mac rolled his eyes and got out of the car, followed by Jack. "Come on," Jack prodded as they walked up to the door.

"Are you ever gonna let this drop if I don't tell your idea was the best?" Mac asked after he knocked on the door. Jack didn't even have to consider his answer.

"No, probably not."

Mac chuckled and opened his mouth, but they heard someone coming towards the door, and he smirked at his partner. "Oops," he said. "It'll have to wait a little while longer."

"Come on dude, it's like five words," Jack griped at his partner. Mac chuckled, but he didn't respond. A few more seconds passed, and he looked at the door in confusion.

"You did hear someone coming towards the door, right?" he asked, leaning across the porch to try and peer through the windows.

"Yeah," Jack replied, also noticing the stillness that had come over the house. He looked at the door a little closer and noticed something. "Dude," he said, smacking Mac gently on the back. When his partner looked at him, Jack pointed to the peephole sitting right above eye-level. Just then, they heard a soft _thud_ come from the backyard, and Mac and Jack immediately ran towards the sound. The two of them rounded the house just in time to see a man quickly climbing over a brick wall leading to the street.

"You go that way, I'll go around and cut him off!" Mac said to Jack before he turned and sprinted the other direction. He tore around a corner that deposited him on the same street Berkhoff had gone to, and when he looked to his left, he saw the ex-agent heading straight for him. The running man was looking behind him to see if he was being followed, meaning he didn't see Mac until it was too late. Berkhoff turned around right before he reached MacGyver, and he tried to stop mid-stride, but he was too late. As he was skidding to a stop, MacGyver held his arms out, letting Berkhoff smash into him. Mac closed his arms, trapping the fleeing agent in a tight embrace while he grabbed his own wrist, trapping Berkhoff in the grip.

"Stop struggling!" Mac said, trying to keep his hold on the wriggling man. Berkhoff jerked his head back, smacking MacGyver right in the nose. Mac reeled back, releasing the ex-agent instinctively as he reached up to clutch at his face. Berkhoff stared at Mac for a second, but turned to run again almost immediately. Thankfully, Mac's attempt to wrestle with him had given Jack enough time to catch up to the two of them, and Jack was bigger than Berkhoff. The ex-agent didn't have much of a choice of where he was going once Jack got ahold of him.

"Listen man," Jack said, struggling with the man in his grip. "We aren't here to hurt you! We work for the Phoen-we work for what used to be DXS," Jack explained. Berkhoff scoffed and continued to struggle, obviously not believing Jack's explanation. "I'm serious dude!" Jack exclaimed. Berkhoff stomped down on Jack's foot hard, but even though Jack let out a short yelp of pain, he kept a firm hold on the squirmy agent.

"Thornton sent us!" MacGyver said, hoping that would stop the man. The words had the desired effect, and Berkhoff ceased his struggling for a moment, looking between the two of them with hesitant eyes.

"Wait, you're MacGyver and Dalton, right?" he asked suddenly as he recognized his pursuers.

"That's right," Mac replied, glad to see that the man seemed to know them.

"Why didn't Thornton come to me herself?" Berkhoff asked, defensive again.

"I guess you've been out of contact with the spy world for a little bit, huh?" Jack said, shaking his head, though he was glad the man had stopped trying as hard to get away. "Thornton was arrested a few months ago; we found evidence that she was the mole."

Berkhoff immediately looked at the two agents, shaking his head. "No way," he said. "There's no way that she's the mole," he insisted. "I went to her first when I found out there was a mole," he explained, steamrolling over Mac and Jack's attempts to speak. "Why wouldn't she have just told me to come home and had me killed? Why wouldn't she have had me discredited or something, instead of putting me in her own witness protection program?"

"Calm down, dude!" Jack finally got across, putting his hand across the man's mouth and giving Berkhoff an extremely exasperated look. "We believe she's innocent," Jack assured him. "We found evidence that should be able to get her name cleared, or at least have her case looked at again," he added.

"So why are you here?"

"Because we have reason to believe that The Organization knows you're alive and are trying to find you," MacGyver replied.

"Who's 'The Organization'?"

"They're the group the mole works for," Jack explained. "Basically they're bad news, and we gotta get you outta here and into protective custody back at HQ; we'll fill you in on any details you need on the way," Jack said, pulling Berkhoff back towards his and Mac's car in front of the house. Once they got to the front yard though, Berkhoff headed towards his house instead of the car.

"Woah woah woah, where're you goin'?" Jack asked, trying to stop the agent. Mac stared at a blue Honda that was parked a few houses down, thinking that he recognized it from somewhere. The car slipped from his mind though as he felt his phone buzz once, indicating he had a notification.

"I'm just grabbing my go-bag," Berkhoff replied, opening the front door.

"No man, listen," Jack said, following the man into the house. "We can get you anything you need when we get back to LA, but for now we need you to just come with us!"

MacGyver had followed the other two into the house, but he was more preoccupied with looking at his phone. When he had started wrestling with Berkhoff, it had apparently switched the phone to vibrate, and he hadn't felt it when it began ringing. He saw he had three missed calls, two from Matty and one from Bozer, along with a voicemail from both of them. He switched his phone back to ringer and was about to call one of them back but was distracted when Jack grabbed his attention.

"Mac, could you explain to Berkhoff why we need to go now?" he asked, barely keeping the frustration in his voice to a minimum.

"Why don't you just pick him up and haul him out of here?" Mac asked with a smirk. Berkhoff's eyes went wide, and Mac continued. "I'm kidding," he assured the ex-agent. The man's eyes didn't go back to their normal size though, and Mac's face fell slightly. "What?" he asked. Before Berkhoff could answer, Mac heard footsteps behind him, as well as the click of a gun's hammer being cocked. He had a sinking feeling that he knew who it was before he even turned around.

"Hands up, and don't even think about going for your weapon, Jack," Nikki said smugly as she came out from behind the corner. She had a silencer attached to the muzzle of her gun, which was aimed directly at Mac's chest. The small group of agents looked around and realized they each had a red dot trained on them as they each raised their arms slowly. They couldn't see the snipers, but Mac figured the gunmen were outside with crystal clear shots.

"If anyone tries to make a move, one of you will be shot," Nikki said. Mac wanted to point out that she didn't really have to explain the whole 'Don't move or you die' scenario, but he figured that now probably wasn't the best time for snark and sarcasm.

"By the way, thanks Mac," Nikki added with a smirk. "We've been searching for Berkhoff for a while now. When we heard he found out about the mole, we tried to get him in Syria, but Thornton beat us to it. I'm impressed with how well she hid him; we really believed that our takedown of his chopper had been successful and that he had died, but recently there began to be rumors flying around about what really happened in exfil. I did some more digging and found out that his body was never recovered, and all the pieces clicked together. We've been looking for him ever since," she explained. "When my men and Thornton didn't make it to the rendezvous point after they picked her up from the hospital, I knew something had gone wrong, and I had a sneaking suspicion that you were behind it," she continued.

"My word, you love to hear your own voice, don't you?" Jack asked snarkily. Nikki glared at him, but MacGyver drew her attention back on himself before she could do anything drastic, like order her men to fire.

"That's why you asked about Berkhoff then? Back in the diner?" Mac asked cooly, making sure his hands stayed up.

"I wanted to see if you knew anything more about what had actually happened to him," Nikki confirmed with a shrug. "I realized you really didn't know anything, so we left."

Mac was about to reply, but his phone lit up and started ringing in his hand, causing everyone in the room to jump slightly. MacGyver kept his hands up, showing that he wasn't going to cause any trouble, but he did look at who was calling; it was Matty.

"Don't answer that," Nikki instructed. The phone stopped vibrating after a few more rings, but almost immediately began ringing again. This time it was Bozer's face that appeared on Mac's screen, and he looked at Nikki.

"If I don't answer this, they're going to know something's wrong," he tried reasoning with her. She smirked at him; her gun was still pointed at his chest, but in an instant she adjusted where it was aimed and pulled the trigger. The shot was barely heard thanks to the silencer, but Mac's phone flew out of his hand in several pieces. He hissed a little in pain and shock and shook his hand, inspecting it to see if he was bleeding. Thankfully, he knew he'd only have a large bruise, and a very sore hand; the bullet hadn't hit him, but his phone was history. He glared at Nikki.

"Now they're going to _know_ something's wrong," he said. "It's just going to give them the busy signal, or tell them my phone isn't in service or something, and they'll know something's up. They'll send help; you know the Foundation, you know how they operate."

"I do know," Nikki agreed. "Which is why I planned for something like this to happen. We're not going to be here when their backup arrives," she stated simply. Mac looked out the front window and saw a large van pull up. The side door opened and men poured out, hurrying towards the house. MacGyver sincerely hoped that Berkhoff had at least slightly nosy neighbors who would notice something unusual going on in the isolated house on the corner, but he was distracted from those thoughts as the front door was forced open. MacGyver made sure he kept his hands up high, but he turned his head to watch several men move towards Jack and Berkhoff. Jack was patted down and had his weapons removed before his hands were ziptied in front of him. Mac turned back around to talk to Nikki, but was met with a taser as soon as he turned his head.

The metal prongs were shoved into the side of his neck and the electricity was turned on, immediately sending shockwaves through the young blond. His knees buckled and he crashed down, colliding with the ground rather hard. Mac thought he vaguely heard Jack yelling, and Nikki's calm, collected reply, and he felt someone grabbing him under the arms and legs, dragging him out of the house. He tried struggling against the men holding him as he saw them nearing the van, but he heard Nikki's voice again and felt the cold prongs of the taser against his neck once more, and his body arched as the electricity raced through him.

His eyes began drooping shut, even though he was fighting against it as hard as he could. He vaguely realized he had been loaded into the van, and he felt his hands being yanked in front of him. Something snug was put over both of his hands before he felt the zipties being tied around his own wrists, but that was the last thing he remembered before he finally gave into the black creeping in on the edge of his vision.

 _ **Not sorry enough about the cliffies though to not leave you with another one... *sheepish grin* sorry... :D**_

 _ **So how obvious was I that it was Nikki? XD I have not hid my dislike for that woman, and I was even talking with helloyesimhere yesterday about what Hogwarts houses we think the MacGyver characters would belong to, and I very simply stated that Nikki was a death eater. *shrugs* XD**_

 _ **So, thoughts?**_

 _ **Pop=Chrysalis**_


	9. Chapter 9

_**Hey hey hey! So I wasn't planning on having this chapter be this long; I was going to cut it off after Mac's part, but it just felt right to keep going, so here we go!**_

 _ **Also, sorry for the slightly later update than usual. This is the beginning of Finals week, and I don't have anything today, so I took advantage of the opportunity to sleep in, and stayed in bed till almost 11.**_

 _ **Anyway...Here's chapter 9!**_

 _ **I don't own these characters :(**_

Matty had a feeling something was wrong the moment Mac didn't answer her second call.

After Mac didn't answer her third call, Matty had Bozer try him one more time. The young man held up his phone to his ear and listened for a few seconds before his face became confused, mixed with worry.

"What?" Matty asked, immediately noticing the distress in Bozer's face.

"I mean, it rang a few times, but then it just...stopped ringing and started giving me the 'phone is outta service' message," the young man explained.

"Riley, get me in touch with the local authorities in Canon City," Matty instructed. Riley nodded and pulled up the contact info, putting the phone on speaker.

"Sheriff Ensign," a voice answered.

"Sheriff, my name is Matilda Webber. I work for an organization in the government, and I have operatives whom we have lost contact with in your city. I'm requesting that you send a team to check up on things and see if everything is alright."

"Sorry, who are you?" Sheriff Ensign asked, frustrated that this woman thought she could just call him up and order him around in his own town.

"Listen, I don't have time to explain," Matty said in exasperation. "Please, just send men over there," she said.

"I'm sorry," he said. "I can't dispatch a team of my men to a spot where we don't have any calls of a disturbance; it wastes time and manpower, when they could be out doing something to help save a life."

Matty's eyes flared. "Listen," she snapped. "My agents are out there and we have lost complete contact with them. They were going to retrieve someone who is vital to national security, but we have reason to believe their mission has been compromised. I am asking you as a personal favor to send out some officers to see if there has been a disturbance, but if you force my hand, I will contact whoever I need to, call in any favors I have, to make sure that you not only get removed from your sheriff's seat, but that you never have a job that holds any power for a long, long time. Do not test me," she said, her voice having gone to a dangerously quiet level. There was silence on the other end for a moment, then Sheriff Ensign came back on the line.

"I'll have men dispatched as soon as you tell me where they're supposed to go," he said, trying his best not to sound too sullen. Matty told the Sheriff where Mac and Jack had been headed, and he promised to send officers out that way immediately. The call was disconnected, and Matty looked at Riley.

"Find anything you can around Berkhoff's house that can help us find MacGyver and Jack," she instructed. "I don't care if it's security cameras, street cameras, a satellite, or even as simple as tracking their phones; just find them."

Riley nodded and began typing away on her computer. Matty stole a quick look at Thornton, who was watching the proceedings with a worried look on her face, biting her lip unconsciously.

"Let us know the minute you find anything," Matty said.

 _0-0-0_

MacGyver woke up when he felt the floor underneath him jolt, and his eyes snapped open. He was glad it was dark, because his head was killing him, and he knew light would have only caused it to hurt worse. He tried moving his hands, but he was unable to, and for a moment, he couldn't remember what had happened. It all rushed back to him in a matter of seconds though, and he sat up immediately, looking around trying to find Jack and Berkhoff. Thankfully, he saw them sitting just a few feet away, and through the dark, he could just make out their faces, looking at him with as much concern as he figured he had on his own face.

"You okay, bud?" Jack asked. Mac nodded his head, but immediately stopped as the action sent a spike of pain through his skull.

"I'll be good," he said, making a mental note to keep his head as still as possible. "How long…?"

"'Bout two and a half hours by my reckoning," Jack said. MacGyver gave him a questioning look, and Jack explained. "Once they got us in the van, they drugged us all with something and knocked us out. Before I passed out though, I heard them mention something about a plane being ready to 'go back,' and I can only assume they're talking about back to California. So once I woke up, I looked at my watch and figured out it's been about two and a half hours."

The floor jostled again, and Mac realized that they were in a moving vehicle, more than likely another van. Mac's eyes had now adjusted to the dark, and he realized that his hands had been ziptied in front of him, and his feet here tied together with duct tape. When Mac tried to flex his fingers, he found that he couldn't move them very far. He looked harder through the dark and realized a pair of mittens had been slipped over his hands. He opened his mouth to ask Jack about it, but the van stopped suddenly, and the three of them soon heard footsteps walking towards the back. The doors were opened and light spilled in, making Mac shut his eyes quickly, even as his head began pounding thanks to the unexpected light.

Hands reached in and grabbed Mac's feet, dragging him forward. Mac struggled a bit, but being tied up made resistance a little more futile. The person dragging Mac forward pulled out a knife and cut through the tape around the blond's ankles before pulling him the rest of the way out. Mac's feet hit solid ground, but before he could even think about running, an arm was wrapped around his neck, pulling him close to a broad-chested man. He felt the cold, oily metal barrel of a gun pressed against his neck, again, and he immediately stilled.

"No struggling, no shooting," Nikki stated simply as she walked around to the back of the van. Mac stared at her. He ignored her shooting comment, instead choosing to focus on her choice of hand restraints.

"Mittens?" he asked in slight disbelief as he held up his hands in front of him. Nikki shrugged.

"I know what you're capable of if you have the use of your hands," she explained. "This just helps keep you a little more...controlled," she said after a moment of searching for the right word.

MacGyver looked around, realizing for the first time that they were on a mountain. He was slightly shocked to see that they were just outside a large, lavish house. He wanted to look around a little more, but movement from the van caught his attention instead.

Jack and Berkhoff were being pulled from the vehicle as well; their ankle restraints were being removed, just like MacGyver's had been. They each had a gun placed against their heads, and once they were able to walk, everyone was shoved forward.

Mac looked to his left, spotting a highway down below them, a steady stream of traffic driving by. He turned his head in the opposite direction, seeing the Pacific Ocean to his right. He looked down the mountain a little ways and saw a house that looked extremely small, but over-the-top decorated, and he suddenly realized where they were. He didn't have time to confirm his suspicions though as he and his fellow captives were shoved forwards towards the front door. Once they were inside the house, Mac saw that it looked bigger on the outside than what it actually was; the ceiling was a lot shorter than he was expecting, and the only reason it looked somewhat large on the inside was because there was hardly any furniture at all in the house.

The prisoners were escorted across the large, almost empty living room to a door on the opposite side of the space. One of the men ahead of them opened the door, revealing steep steps that led down to what Mac could only assume was the basement. The three captives were pushed towards the stairs, Mac in the lead, right behind the man who had opened the door. Mac began stepping down the steep steps, but it was dark and his head was still throbbing slightly from his encounter with the taser, making him not watch where he was going as carefully as he should have been, and he missed a step. He let out a startled grunt as he began falling down the stairs. Thankfully, since his hands had been restrained in the front, he was able to catch ahold of the railing before he fell down too many stairs, though the force of his body stopping yanked on the zipties and causing more pressure to his already-bound limbs. The mittens on his hands prevented him from getting an extremely good grip on the railing, but it was tight enough that he stopped falling.

"Mac! You okay?" he heard Jack ask from behind. The blond began pulling himself to his feet, using the railing as support and wincing as the zipties dug even more into his wrists.

"I'm good," he replied. He had a bump on his head and he was sure that his knees were going to be bruised as well, but other than that, he had stopped his fall before any serious damage was done. He felt a strong hand grab the back of his shirt and guide him down the rest of the steps, as if they were worried he was going to fall again.

Once they all got downstairs, the prisoners were pushed forward to three waiting chairs. They were sat down, and immediately they had guns placed at the backs of their heads, stopping any ideas of trying to make a break for it. Nikki walked in and stared at each one of them in turn. "I think you know what happens if you try to escape?" she asked, smirking at the men sitting in the chairs.

"You won't shoot us," Mac said, shaking his head slowly. "If you had wanted us dead, you would have killed us back in Colorado. You need us for something."

"You're right," Nikki agreed. "But I really only need you or Jack for leverage if I'm being honest," she explained. "Berkhoff is going to die, but you two are my bargaining chips. If one of you gets shot along the way, as long as I have the other one, I'll still get what I want. If I'm being honest though," she said as she crouched down next to Mac, placing her hand on his knee. "If someone's going to die, I don't want it to be you. No offense, Jack," she said, looking over at Jack.

"Full offense taken," Jack snarked back. Nikki looked back to MacGyver, shrugging her shoulders.

"I can't believe you," Mac said, shaking his head. "It was all a lie, wasn't it?" He was having deja vu moments back to the first time he confronted Nikki about her feelings for him, back when she stole that virus. He realized that he had known for a while that Nikki still wasn't who she said she was, but having those suspicions confirmed just added salt to the wound.

"Like I told you before," Nikki said, sounding slightly hurt. "My feelings for you are real," she insisted. "We just have different ideas about what's right and what's wrong. The government needs to be stopped, Mac," she said. "They're out of control, and we're simply trying to put power back in the hands of those who deserve it!"

"The people you think deserve it don't know what to do with that much power, and they'd ruin themselves faster than you could blink if they were given all the power," Mac argued. "While I don't agree with everything the government has done, or is doing, you can't seriously think that giving the power to someone else is in America's best interest, can you?"

NIkki gave her ex-boyfriend a pitying look, but she didn't say anything else on the matter. She stood up and motioned at someone behind the captives, and the prisoners heard people behind them moving forward.

"I'll see you boys later," she said, trailing her fingers lightly along Mac's shoulder as she walked away. Mac wished he could jerk away, but the best he could do was simply squirm out of her reach as much as possible. "Keep them in line," Nikki instructed one of the men behind them.

"Yes ma'am," the man replied. He walked around to the front of the prisoners, and they saw that he was carrying a video camera and a tripod, which he set on the floor facing the three agents.

"We're gonna have ourselves a little video shoot," he said.

"Sorry, could you get this side?" Jack asked, turning in his chair as much as he could. "It's my good side."

The man smirked at Jack before lashing out with a wicked left hook, whipping Jack's head to the side. The older agent looked back around, spitting out a bit of blood as he looked up at the man who had punched him.

"That smart mouth is gonna get you into a world'a hurt," the man said in a slightly threatening tone.

"Been there, done that," Jack replied, spitting a little more blood out, near the boot of the man. The man looked like he was going to do something else violent, but one of his buddies called out to him, distracting him for a moment.

"Hey Terry," one of the men behind them called. Terry looked up, lifting his hand to catch a cord that was tossed his way. That short moment gave Mac a quick opportunity to think of some way he could try to get word out to where they were. He knew what the 'video shoot' was going to be; it was a sort of ransom trade, except instead of trading money for people, it would be an exchange of people for people. He and Jack for Thornton, though he was pretty certain The Organization wasn't going to actually give him and Jack back. That just meant that they had to find some way to help themselves.

Before Mac, Jack, or Berkhoff could even comprehend what was going on, a rag was wrapped around their mouths, a knot securely tied at the backs of their heads. "Just so you don't get any ideas about letting people know where we are," Terry explained as he set up the rest of the recording equipment. Arms were also wrapped around the prisoner's necks and the guns were moved from the back of their heads to the sides of their temples. Once Mac saw the flashing red light and heard Terry begin naming their demands, Mac began blinking out a pattern to let whoever the video was being sent to know where they were.

 _I know, it's a bit of a long shot, but if someone was able to recognize my morse code when I was trapped in the trunk of El Noche's car, I'm hoping someone will recognize this. And honestly, right now hope is all we've got._

 _0-0-0_

"Sheriff Ensign, tell me you've got something," Matty said as they answered the Sheriff's call.

"I'm sorry, but by the time my men got there, no one was at the house. It does look like there were some small signs of struggle, and when we talked to the neighbors, some of them say they remembered seeing an unfamiliar van in front of the house, but no one got a plate number," he said apologetically. Matty sighed; that was nothing new to them, thanks to Riley. She had tried tracking the van, but she lost it in traffic a few miles before Colorado Springs. Riley _had_ been able to pull plate numbers, but the plates were fake, and the van was a common Chrysler make and model, with thousands of them registered in the state.

"Thank you for your help," Matty said resignedly.

"Sure thing," the sheriff replied. "Sorry about your agents; I'll let you know if anything turns up," he promised, though he had a sneaking suspicion that nothing was going to turn up.

"We appreciate it," Matty said before she ended the phone call. The director of the Phoenix Foundation got on her phone and began talking with different teams who had been sent to Colorado to search for the missing agents. All of them reported the same thing: there were no signs of MacGyver, Jack, or the package they were supposed to be picking up. Matty hadn't given anyone on any of the teams specific details about what 'the package' was; she knew that if they found Mac and Jack, they'd find Berkhoff, so there was no reason to give away Berkhoff's identity until it was absolutely necessary.

They continued running searches for the next two and a half, almost three hours, trying anything they could while keeping in contact with the agents in Colorado. Riley was currently running pictures of the three missing agents through any cameras she could find and looping the feeds back to her computer so that she could run facial recognition, but everything she was trying was coming up empty. She even tried running Nikki's face through the database, but no matter where she looked, she couldn't find any trace of her friends. As she was searching, a notification popped up on her screen, indicating an incoming email with a video attachment.

"Matty," Riley said as her computer dinged. Matty turned to face Riley, and the young hacker threw the email up onto the screen so that everyone was able to see. Bozer and Thornton looked at the screen as well, and once everyone was looking, Riley clicked on the attachment, bringing up the video.

The scene that was presented before them wasn't a surprise to anyone, but it was still slightly shocking to see MacGyver and Jack, sitting next to whom everyone assumed was Berkhoff. They all had rags in their mouths with guns pointed to their heads as a voice from behind the camera started speaking.

 _We know you have Thornton, and we know you've been gathering evidence trying to disprove that she's Chrysalis. As you can see, we have your agents, but we're willing to make a trade. You give us Thornton and whatever evidence it is you think you've collected, and we'll give you back MacGyver and Dalton. We'll be sending some coordinates in a few minutes, and we expect you to be there at three p.m. sharp. If you aren't there, your agents will die._

The video cut out, and Matty looked at Riley, who was busy typing away at her keyboard. "Please tell me you were able to trace where that email came from," the director said.

"I'm trying, but they used a similar code to the one that jumbled up the IP address numbers like they did when Nikki was chatting Chrysalis," she explained.

"So can't you just use the same program you did earlier to un-jumble the numbers?" Matty asked. Riley nodded.

"I can, but they tweaked the program enough that I have to tweak _my_ code in order to get it to work," Riley replied, already busily typing away at the new code. Matty nodded; she knew Riley was doing her best. They played the video a few more times, trying to discern anything they could about where Mac, Dalton, and Berkhoff were being held, but after watching it for the fourth time, they still had no clues whatsoever. They could tell the three of them were in a basement, but there were no windows to let them see scenery outside that might give them a clue.

"Riley, could you send this over to the labs and have them begin analyzing the video itself while you're working on the IP code?" Matty asked.

"Sure," Riley said, forwarding the email down to the labs with Matty's instructions. While the hacker was taking care of that, the director walked over to Thornton and undid the restraints on her wrists.

"I think it's okay to let you out of these now," she said as she released the dark-haired woman. Thornton muttered a quick thanks and began rubbing her wrists, but she wasn't really paying attention to anything except the screen, where the last frame of the video had been paused.

"What's wrong?" Matty asked, staring at the screen as well.

"Could you play it again?" Thornton asked. Riley looked a little confused, but she did as her old boss requested, starting the video over one more time. Everyone switched their gazes between the video and Thornton as she watched the screen with unwavering concentration. The video ended and everyone looked at Thornton expectantly. Her eyes held a triumphant gleam in them.

"Care to share with the class?" Matty asked.

"Mac's blinking," Thornton replied.

"Yes, blinking is a normal human function," Matty said, trying not to sound as sarcastic as she wanted to.

"No, he-Riley, play the video again, but this time look at MacGyver's eyes," Thornton directed. Riley did as she was told, and they all watched the blond. After a few moments, they were finally able to see what Thornton had pointed out.

"Is that Morse code?" Bozer asked, squinting at his partner's blinking patterns.

"No," Thornton replied. "It's not morse, but it is a code. It's the five-across five-down pattern," she explained. Matty immediately recognized what the code was, but Riley and Bozer continued to look confused.

"The what now?" Riley asked, pausing in her typing for a minute.

"If you put the alphabet in rows of five, it comes out to five rows and five columns," Thornton explained.

"No offense Thornton," Bozer interrupted. "But I think you're forgetting something; the alphabet has twenty-six letters," he reminded her. Thornton nodded, then continued.

"You're right, but a lot of times the letters 'K' and 'C' make the same sound, so the 'K' is left out, and they just replace it with a 'C,'" she explained.

"She's right," Matty agreed. "It's not something that I've seen used in a long time, but now that you point it out, it's definitely what Mac is doing," she agreed. "Riley, play it one more time, and this time we're going to find out what Mac is trying to tell us."

The video started once again, and everyone watched.

"Four blinks, a small pause, then three more," Bozer reported.

"That's an 'S,'" Thornton replied almost immediately.

"Opposite now," Riley said. "Three, then four."

"'O,'" Matty muttered. They continued watching the video up until the end, and they were able to get the letters 'L,' 'E,' and 'D' before the video ended.

"S.O.L.E.D.?" Bozer asked once the video ended. "What kinda message is that? Is he tryin' to tell us they're being held somewhere that was just _sold_? We may need to work on Mac's spelling skills if that's the case," Bozer added. Riley's eyes went wide and she immediately went back to her computer, drawing the attention of Matty.

"What is it, Riley?" the director asked.

"I think I know where they're being held," Riley said, sounding slightly distracted as she pulled up a file running in the background on her computer. "Ever since we realized it was Nikki's voice on the phone, I've been monitoring her bank account activities," Riley explained.

"And? Did we get a hit?" Matty asked.

"No, but that's what I realized the problem was," Riley said, sounding excited as she began to explain her thought process. "There'd been no activity in her accounts whatsoever, meaning she's either paying cash for everything, or she's got a way to pay for something through a shell company, or an LLC that we weren't aware of. I did a bit of digging, and I found an offshore account under a Management LLC; when I looked into it a little further, I found that the manager of the account is one of Nikki's aliases from those passports we found when she was first arrested."

"Did you find anything in that account?" Thornton asked, her instincts as director taking over. She shot Matty an apologetic look as she realized what she had done, but Matty waved her off.

"It's fine," she said, sounding like she didn't care at all that Thornton had just slipped back into director mode. She was more focused on finding out what Riley knew. "Did you find any activity that would help us find where she is?"

"Not anything recently," Riley admitted. "But I did find something, though it didn't mean anything to me until just now. There was a house that was purchased a few months ago using that Management LLC. It's a large home on Mt. _Soledad_ , in La Jolla," Riley finished. Matty nodded and immediately got on her phone.

"This is Director Webber. I need agents dispatched to Mt. Soledad," she said. "The exact address will be sent to you in a few minutes, but I need you to start heading out now." She turned off her phone and looked at Riley and Bozer. "You two need to stay with Thornton," she instructed. Riley and Bozer's jaws fell open and they both immediately began protesting, but Matty silenced them with a stare.

"Guys, I need someone to stay behind with Thornton, and you two are the only ones I trust to stay with her. We don't know who could be part of The Organization, and I need her kept safe. Riley, you're the best person we have on computers to guide us and watch our backs. Bozer, I know you want to help, but you haven't received enough field training for me to feel comfortable having you out there with us. I promise, we're going to bring them home," she said, her tone indicating that she wasn't going to accept any counter arguments. "I'm sorry," she said, actually sounding apologetic. "But that's all I'm going to say about it. Riley, I need you to send me that address," she added.

Riley nodded, and both she and Bozer looked sullen as Matty walked out, leaving the two agents with their old boss.

"It'll be okay," Thornton said, trying to assure the two younger people. "Matty's as good as they come; she'll make sure everyone stays safe," she promised. Riley and Bozer nodded; they knew Matty wouldn't let anything happen to their friends if she could help it, but they were worried all the same.

Truth be told, Thornton was itching to get out there and help, and she was half tempted to try and convince Bozer and Riley that the three of them should sneak out and go help, but she knew that for Matty's logic was sound as to why she left them behind. Thornton had been shot and operated on less than forty-eight hours ago, and Bozer had (to her knowledge, anyway) no experience in raid/hostage situations. As for Riley, while she did normally go out in the field with Jack and MacGyver, Thornton understood why Matty wanted her to stay behind and monitor things from the base. The three of them would honestly be a liability in the field, and would more than likely jeopardize the mission more than they could help if they disobeyed Matty's orders. So for now, they would do as they were told, and manage things from Phoenix headquarters. That didn't mean that Thornton was planning on sitting back and doing nothing though.

 _ **Well well well...looks like the boys have backup coming for them!**_

 _ **So the code that Mac used, I don't know if it's actually a thing, I stole it from The Flash. From what I remember, I did some research about it for another story I wrote (that will never probably see the light of day) and it was actually a thing, but I don't remember exactly, so I didn't make it up. You guys can thank The Flash for it ;)**_

 _ **Also, what with it being finals week, I didn't have anything today, but I do have stuff tomorrow and on Wednesday, and possibly something on Thursday, so I may not be able to update until Thursday night or Friday morning. Just letting you all know :)**_

 _ **Thoughts? Lemme know what you think!**_


	10. Chapter 10

_**I'm back! Sorry for the wait, I ended up moving home a week earlier than I was expecting, so I spent Wednesday and Thursday after my finals packing and then moving down, and I stayed up with my sister last night until like, 1 in the morning (Whereas I'm usually in bed by like, 11 at the latest XD) but! I'm back, and should be back to normal posting schedule :)**_

 _ **Also, this is now officially my longest story yet! It just passed 30k words! *insert screaming emoji* Thank you all for the support you show me and this story! You guys are the best :)**_

 _ **None of the characters belong to me, sadly.**_

Forty minutes after Matty and her team left, Riley, Bozer, and Thornton were all sitting in the war room. Thornton had moved from her bed to one of the couches, though she was still moving gingerly, and Bozer had tried to convince the woman to stay lying down. "I just need a change of position," Thornton insisted as she lowered herself down. "I know my body's limits," she assured the young man. He still looked skeptical, but he knew better than to try and argue with Thornton. "Riley, can I have a phone?" Thornton asked. Riley pulled out her cell and handed it to her boss.

"Who're you calling?" the young woman asked as her old boss dialed a number.

"One of the only other people I trust completely to bring Mac and Jack back," Thornton replied. Riley began wracking her brains trying to think of who Thornton could be referring to, but she didn't need to wonder for very long. "Sarah, it's Patricia Thornton," she said when the call was answered. Thornton put the phone on speaker so that everyone could hear what was going on.

"Patricia, hi," Sarah said, sounding confused. "Where's Matty?"

"She's not here right now. Sarah, how much do you care about Jack?" Thornton asked.

"Why-what does that have to do with anything? Why are they letting you use a phone? Where's Matty?" Sarah asked, barely pausing for breath. Riley held out her hand, and Thornton placed the phone in the hacker's palm.

"Sarah, it's Riley."

"Riley, what is going on?" Sarah asked. "Why is Thornton on the phone? Why is she asking about Jack? Where did Matty go? Why-"

"It'd be easier to explain if I could talk," Riley pointed out. Sarah stopped talking, and after making sure she wasn't going to start firing questions again, Riley answered her already-existing questions. "Thornton is on the phone because for the time, she is no longer the main suspect as Chrysalis. She's asking about Jack because we just got a video from The Organization, and they've captured Mac, Jack, and another agent, and they're wanting to trade them for Thornton and the evidence we've gathered to clear her name. We were able to find out where they're keeping Mac and Jack hostage, and Matty went out with a team. It wasn't a big team though, and we were wondering if you'd be able to take the people you trust the most and go help get our guys back?"

There was silence on the other end of the line as Sarah took in everything Riley had said. "Of course," she finally replied. "I can get a small team together, and we can be on the road in ten minutes," she promised. "And don't worry; I'd trust these people with my life," she assured the younger woman.

"Good. We need all the people we can trust. I'm sending you the location now…" Riley muttered as she texted the location to the CIA agent's phone.

"Got it," Sarah responded after a minute. "We're only about twenty minutes away from there," she added as she looked at the location.

"Yeah? Then you should be getting there just around the same time Matty and her team does," Riley said.

"We'll be on the lookout for them," Sarah said. "Don't worry. We'll bring everyone home safely."

"Sarah," Riley said before the call was ended. "One more thing. Nikki Carpenter is going to be there. We have reason to believe that she's the one who grabbed Mac and Jack."

"Got it," Sarah said, not really sounding surprised at all. "We'll keep you updated," she promised.

"Thanks," Riley said. With that, the phone call was disconnected. Thornton and Bozer looked at Riley, who walked over and began pulling up all camera footage she could find of anywhere near Nikki's house on Mt. Soledad. The team was going to need all the help they could get, and it was Riley's job to make sure they knew what they had to be prepared for.

 _0-0-0_

It had been about an hour since the video message had been sent, and the three prisoners were beginning to go slightly stir crazy. Their gags had been removed, but after Jack's constant talking, the men guarding them threatened to put the rags back in their mouths if he didn't shut up. Jack quickly closed his mouth, though it didn't stop him and Mac from communicating through looks and expressions.

After about an hour and fifteen minutes, Terry's phone began ringing. He he answered it, and there was a moment of silence as he listened to who Mac assumed was Nikki on the other end of the line.

"Understood," he said before hanging up the phone. "Come on," Terry said, addressing his companions. "Two black sedans were just spotted heading up the mountain," he explained. "Nikki says that she knows without a doubt it's Phoenix, and we're supposed to get upstairs right away."

The men started walking away, and Jack turned around in his seat seat slightly. "Aren't you takin' us with you?" he asked. There were a few scattered chuckles, and then Terry answered.

"Oh, we'll be back for you, I'm sure," he assured the Texan. Jack didn't like the way the man's voice sounded as he said that, and he voiced as much once the guards had ascended the stairs and shut the door, leaving the three of them in the dark.

"This obviously isn't what was supposed to happen," he pointed out. "Matty and the team are disrupting their plans. We have to find a way outta here before they come back and kill us," he encouraged Mac.

"Jack," Mac interrupted his partner. "I have an idea, but I need your help."

"Uh, I'd love to, but I'm just as tied up as you are, bud," Jack reminded his partner, wiggling his bound hands.

"Not quite," Mac replied, holding up his hands and nodding at the mittens covering his hands. "If I didn't have these mittens on, I'd do this myself, but as it is, I'm going to walk you through how to get out of your zipties," he explained.

"I'm all ears," Jack said.

"How is he going to do that?" Berkhoff asked, his voice startling Mac slightly, as it was really the first time he had heard the man speak since they had been grabbed. "He doesn't have a knife or anything to cut it with!"

"Well, as long as we've got friction on our side, I don't think he'll need a knife," Mac explained.

"Just trust him, man," Jack assured Berkhoff. "He's gotten us out of tighter situations than this before. I've learned to just go with whatever Mac's gut is feeling; it's usually on the right track. Whaddya need me to do, bud?"

"First, you need to untie your boot laces, both of them," Mac instructed. Jack gave his friend a puzzled look, but remembering what he had just said to Berkhoff, he didn't question it. He lifted his feet up onto the chair he was sitting on and began untying his laces. Once he had done that, he looked at the young man expectantly.

"Now," Mac continued. "Tie the laces together through your zipties."

Jack did as he was told, though it took a little longer than he expected. Maneuvering his wrists while they were tied together was challenging. Finally though, Jack accomplished the task of tying his shoelaces together through his restraints.

"What now?" Jack asked, beginning to shake slightly as the position he was holding himself in began to put an awkward strain on his body.

"Move your feet," Mac replied. "Pretending like you're riding a bike," he added. Jack looked at him slightly skeptically, but he once again remembered what he had told Berkhoff mere minutes before, about trusting the young blond, and he began moving his feet like he was riding a bike. A few seconds passed, and then with no warning, the plastic ties around Jack's wrist snapped. Jack's feet hit the ground, and his hands flew up and smacked his face, thanks to the fact that he had been resisting so he could cut through the restraints faster. Mac couldn't help the snort that escaped when Jack's hands flew into his nose, and the older agent glared at his partner for a minute.

"Sorry," Mac said, clearing his throat, but not actually looking apologetic at all. "Okay, now all you need to do is-"

"Find something to get your zipties off, yeah," Jack said, looking around. He spotted an empty champagne bottle in the corner, and he got off his chair and walked over to grab it. Jack held the bottle in his hands, squinting at it and holding it up to the light.

"Too bad there's nothin' left in here," Jack commented, popping the cork off and peering through the bottle opening with one eye.

"Jack," Mac said, somewhat exasperatedly. "Any time now would be appreciated," he reminded his partner with raised eyebrows.

"Calm down," Jack said as he shrugged off his jacket and wrapped it around the bottle. "Those five seconds aren't gonna make much of a difference," he pointed out.

"They could!" Mac argued.

"Give me one good example where five seconds could make that big of a difference," Jack challenged as he smacked the jacket-covered champagne bottle against the wall. The jacket muted the sound of the glass breaking, and Jack began fishing through the assorted pieces of glass. Mac opened his mouth to give Jack an answer, but he shut it again almost immediately. He could think of several times that five seconds could make a difference, but most of them were science-based, and Mac was one hundred percent sure that Jack wouldn't understand what he was talking about, so the blond just decided to not argue with the older man.

Jack walked over with a decently large piece of glass in his hands, and soon MacGyver's wrists were free, and he was pulling the mittens off his hands. Jack walked over and freed Berkhoff as well, and the three of them stood in the basement, looking at their surroundings.

The basement was actually more furnished than most of the rest of the house that Mac had seen; there was a gas fireplace, and a desk with the computer they had sent the video email with, a couch, the chairs they had just been sitting in, and a table. Mac hurried over to the computer and wiggled the mouse to wake the screen up, but the computer was locked. Mac tried all the passwords he could think of that Nikki might use, but none of them worked. He finally stepped back, huffing in frustration. He looked up the stairs at the door, where he was sure there was at least one man standing guard.

"Mac?" Jack asked. "You got something?"

"I mean, it's nothing fancy," Mac replied. "Part of it is probably more along your line of thinking actually," he added.

"Hey man, the simpler, the better," Jack said, clapping his friend on the shoulder. "And by 'my line of thinking,' you mean…?"

"It's not going to be subtle or quiet," Mac clarified.

"Okay, that's not necessarily just my line of thinking," Jack defended. "You've had some pretty loud ideas before," he reminded his partner. MacGyver was about to respond, but their third companion interrupted them.

"What do we need to do?" Berkhoff asked.

 _ **Okay, so I know this probably wasn't my strongest chapter, but *shrugs helplessly* I've been struggling writing the past few days/weeks, so I hope it's okay!**_

 _ **Lemme know what you thought?**_


	11. Chapter 11

_**Hey! Sorry the update is so late. Now that school is out, I'm back to work full time, so updates will more than likely be in the late afternoon/evenings instead of the mornings for the foreseeable future. Anyway, here is the next chapter!**_

 _ **So I'm not sure what's up with fanfiction, but it hasn't been sending out email notifications. Hopefully it's fixed, but if not...I'm sorry :/**_

 _ **Anyway. Onto chapter 11! I think there are only one or two chapters left, so we are coming to an end... I hope you've liked the story so far!**_

 ** _I don't own these characters_**

"Are you sure this is going to work?" Berkhoff asked as he watched MacGyver and Jack walk over to the table. Jack chuckled softly.

"Listen, usually when Mac says he has an idea, it involves him combining a bunch of chemicals with names that I can't even pronounce, and half the time he doesn't know if it's gonna blow up in our faces or not. This?" he asked, gesturing to the table they were lifting up. "He was right. This is more along the lines of my thinking."

"You guys ready?" Mac asked, interrupting their conversation.

"Yup," Jack replied. MacGyver and Jack lifted the table off the floor and walked up the stairs as quietly as they could while Berkhoff followed behind them. Once they neared the door, Mac and Jack stopped moving, and Jack set his end of the table down.

"I mean, are they really going to fall for this? You really think they're going to open the door?" Berkhoff whispered, trying not to sound skeptical. He'd heard about MacGyver and his crazy inventions that saved the day, but this wasn't one of those inventions. This was simple and straightforward, which wasn't a bad thing; it just wasn't exactly what Berkhoff had been expecting.

"The way I see it, they're going to know something's up, and they're going to want to come investigate, or at least try to keep us in line. The door opens outward, so we can get as close to the door as we want, and then when they open it, we make our move," Mac explained simply. "But you know what," he added as he looked back down in the basement. "We'll need something to restrain them once we're out," he said. "Jack, don't do anything yet," he instructed before quickly slipping back down the stairs and hurrying over to the desk with the computer on it. He looked behind the monitor and found all the different plugs and such, and he ripped them out and stuck them in his pockets before making his way back over to his end of the table. Once he was in position, he nodded at Jack. Jack immediately turned around and began banging on the door and yelling.

"Hey! Hey you out there! I know you can hear me! You shoulda tied our feet to the chairs if you didn't want us up and wandering around!"

They heard some disgruntled noises coming from the other side of the door as Jack moved away and grabbed his end of the table. He and Mac hoisted the wooden piece of furniture up as they heard a key being inserted into the lock on the outside, and as soon as the door swung open, the two Phoenix agents charged forward. They rammed the door the rest of the way open with the table and swung it around, crashing into everyone who was in their way. Once Berkhoff was clear of the room, Mac and Jack dropped the table with a loud _thud_ and moved to face their guards one-on-one.

There had been five men in the general area of the door when the prisoners made their escape, but Mac and Jack had taken out two with their table, leaving three guards left, one for each agent.

One of the men reached for Berkhoff, but he simply sidestepped the grabbing hands and delivered his own wicked left hook, stunning the guard for a minute. Berkhoff took advantage of the man's moment of shock to kick his chest, knocking the guard to the floor. After that, it was a simple matter of one more punch to the face before the guard was unconscious on the floor.

Jack met his attacker head on, and the two of them looked like they were in a wrestling match. There was a pop, and Jack reeled back, clutching at his nose and glaring at the guard he was fighting. He drew his hand away for a minute, glad to see that it wasn't bleeding, but he had to quickly forget about his nose as the guard charged him again. This time, Jack caught the man's fist and quickly twisted himself so that his back was to his opponent, and with one swift downward motion, there was another _pop_ , but this time it was Jack's attacker who was the victim. Before he could yell in pain, Jack quickly flipped the man again and gripped him in a headlock, squeezing until the man went limp as he fell into unconsciousness.

The last guard grabbed Mac around the neck, but the blond simply bent forward, using the momentum of the guard's attack to dislodge him. Once the man was on the floor, Mac got on one knee and introduced his fist to the guard's face. He made sure the man was unconscious, then he rolled him over and pulled one of the computer cables from his pocket, using it to to secure the guard's wrists together behind his back. Once his attacker was restrained, Mac moved on to the other guards.

"Really?" Jack asked as he looked around at all the downed men, sounding rather disappointed. "You weren't even skeptical when I _alerted_ you to the fact that we were doing something we probably weren't supposed to be doing?"

"I don't think they're going to be answering you, Jack," Mac pointed out as he finished tying the last guard's hands together. Once he finished tying the last knot, he stood up and looked around. The three of them quickly made their way through the house, coming to the living room they had been led through when they first arrive.

They hurried across the room and over to the front door, quietly opening it and creeping out, keeping an eye out for agents from either side. MacGyver was a little concerned that they hadn't seen any other agents from The Organization, but he almost immediately wished he could retract that thought as he heard a gun click behind him.

"Stop," Nikki ordered. MacGyver stopped running, groaning internally as he held his hands out to his side and turned around, motioning for Jack and Berkhoff to do the same thing. Nikki was alone for the moment, but MacGyver was sure that wasn't going to last very long, and he knew he had to act sooner rather than later.

"You've lost, Nikki," Mac said as he faced his ex. "We heard your men; Phoenix agents are gonna be here in a matter of minutes. Even if you kill us, you won't be able to get away," he said, trying to reason with her. "Just turn yourself in. Don't add murder to your sentence."

"I'm already going to be locked away the rest of my life," Nikki countered, not lowering her gun. Her hand was shaking, though it was almost imperceptible, but Mac saw it. He took a small step forward, bringing his hands to rest at his side.

"Nik," he said quietly, though he almost shuddered as he used her nickname. "What do you gain by killing us?" he asked. Nikki shifted slightly from one foot to the other as she considered the man in front of her. "They already know Thornton's not Chrysalis. If they don't know it's you now, it's only a matter of time before they do find out," Mac added. "It's not worth it."

Nikki chewed her bottom lip. "You may be right about it not being worth it to kill you and Jack," she finally admitted. "But Berkhoff?" she asked, adjusting her weapon so that it was aimed at the agent everyone had thought was dead for so long.

The world seemed to move in slow motion; Nikki's gun began moving, and Mac lunged forward and collided with her right as a shot rang out, and Berkhoff let out a strangled cry. MacGyver wrestled with Nikki on the ground for a minute before he was able to yank the gun out of her hands. He quickly stood up and tossed her gun to Jack, who immediately trained it on the woman still on the ground while Mac turned his attention to Berkhoff. The man was lying on the ground, clutching his upper thigh, which was quickly becoming more and more red as blood seeped its way across the man's pants.

"Okay Berkhoff, I need you to hold still," Mac said, immediately undoing his belt as he knelt down next to the injured man.

"Just get the bleeding stopped," Berkhoff groaned through clenched teeth. Mac quickly examined the wound, and was grateful as he realized the bullet hadn't hit the artery in Berkhoff's leg. He quickly wrapped his belt around the wound and tightened it as much as he dared, causing the injured man to groan in pain again.

"Sorry," Mac apologized. He knew how much pain Berkhoff was in, and he wished he had some sort of numbing agent on hand, but he knew the most important thing at the moment was to stop the bleeding.

"Hey Mac," Jack said, throwing a quick glance behind him. "We got company!"

For a minute, MacGyver feared that Jack meant Nikki's men had finally caught up with them, and while he looked up and saw Terry approaching, he realized the 'company' Jack was referring to were the eight people clad in black coming from the opposite side, led by Sarah Adler.

"Are you guys okay?" she called out as they neared.

"He needs to get to a hospital," Mac called back, moving aside so she could see the injured agent. "He's losing a lot of blood, and the belt can only do so much damage prevention."

Sarah motioned her men to move forward, and they immediately made their way towards the three agents. MacGyver backed up as they reached him, giving them room to extract Berkhoff.

"Are you two okay?" Sarah asked, getting closer to them with every step.

"Yeah, I think we're good," Jack replied, glancing back at Sarah as he answered. MacGyver also turned to look at Sarah for a quick minute, leaving no one watching Nikki.

"Mac, look out!" Sarah yelled. Mac tried to turn back around, but a blow to the back of his head left him seeing stars, and things began splitting into two. He fell to his knees, and he felt something hard press into the back of his head, right above where he had been hit, causing an unnecessary amount of pressure and pain in that area. He reached his hand up to feel the back of his head instinctively, but he felt the gun press harder, convincing him to stop moving.

"Stop!" he heard Nikki yell. "Stop or I swear he's going to get a bullet in the brain!"

"You wouldn't do that, Nikki," Jack said in a coaxing voice. "You've said it before: You really do, or did, love Mac, and I don't think you'd be able to pull the trigger if you wanted to," he pointed out.

"You're right," Nikki said after a moment. "I won't pull the trigger. But _he_ will," she finished, and Mac felt a large hand grab the back of his neck, making him wince in pain. He was hauled to his feet by whom he assumed was Terry, and a gun was placed against his head.

"You won't have Mac killed," Jack said, keeping his gun trained on her. "When we first found out you were alive, Kendrick told us you didn't want Mac dead. Even then, it's only pure luck that the bullet barely missed his heart, and he still had to go on leave for three months because of it!"

"I don't _want_ him dead," Nikki agreed, ignoring the rest of Jack's tirade. "But if you follow me, or try to stop me, you'll force my hand, and I _will_ have him killed."

Jack kept his gun trained on Nikki, but the woman could see in his face that he wasn't going to stop her, and she began to back away while Terry brought the blond along with them. Mac had his hands out to the side, but he knew if he left with her, he wasn't going to see any of his friends again. He could feel the gun still pressed against the back of his head, meaning Terry was in close proximity. Mac only thought about his actions for a minute before he moved. He spun and swung his arm around, connecting with Terry's wrist and knocking the gun away from his head. Mac began wrestling with the man for the gun, the two of them struggling to gain the upper hand.

Jack watched his partner fighting with Terry, and he desperately wanted to take a shot at Terry or Nikki, but Terry kept moving and Jack knew he didn't have a clear shot; he'd run the risk of hitting his friend instead. Nikki was standing behind the struggling pair, conveniently placing Mac and Terry in front of herself, meaning once again, Jack was unable to take a clear shot. He kept raising and lowering his weapon slightly, trying to decide if he should take the shot or not, but suddenly the tables turned, making Jack's decision for him.

Mac fought with Terry for a few more moments, but suddenly Terry's knee appeared out of nowhere and buried itself in Mac's gut, making the blond double over with a wheeze. Terry reached for the back of MacGyver's shirt, but Mac shot back up, placing a well-aimed knee in between Terry's legs. When he bent over in pain, Mac's fist was there waiting. Terry jerked backwards and Mac took advantage of his distraction and tackled him, twisting and turning while Terry fought back. They ended up a tangled mess of limbs, Mac's legs wrapped around Terry's torso while Terry reached up and grabbed Mac's neck, pulling the blond forwards. Mac gripped Terry's wrists and tried to pull them off, but when that didn't have the desired effect, he found a pressure point in the man's wrists and pressed hard, causing Terry to grunt in pain and release Mac's neck instinctively.

MacGyver immediately tried to wrap his own elbow around his opponent's neck, but a gunshot exploded near his shoulder, and he flinched away, loosening his grip slightly on Terry. That gave the other man the chance to wriggle the rest of the way out of Mac's hold, and he quickly stood up, leaving Mac laying on the ground with his hands raised in a peaceful gesture, staring at Nikki as she levelled her gun at his face.

"Next one goes in your head, Mac," she warned.

"Listen Nikki," Jack said in a calm voice as she continued to aim her gun at MacGyver. "This isn't gonna help anything. You know you can't go anywhere that I won't find you if you do anything to Mac," he promised.

"Hurting Mac is the last thing I want to do," Nikki assured Jack. "But if you try to stop me from leaving, I will do what I have to do."

Jack spotted something behind Nikki, and he started moving forward slowly. Nikki cocked the gun again.

"I'm serious Jack," she said, pushing the gun towards Mac slightly.

"I don't think you're gonna to do it," Jack said confidently, taking another step forward.

"Jack," Nikki said, almost in a pleading voice. Mac stared at Jack with an expression the older agent couldn't quite read-it was a mix between confusion, worry, and panic, but there was also a strong sense of trust in the blond's features. Jack locked eyes with his partner, who gave a small nod, and Jack continued forward slowly. "Jack," Nikki repeated. "I _will_ do what I have to do in order to get away," she repeated. Jack weighed his options, took one more step, and a shot rang out. There was a yell of pain, and Nikki fell to the ground, clutching at her arm.

"And I'll do what I have to do to keep my agents safe," Matty said firmly as she walked up. She was still holding her gun out in front of her, and she stared unsympathetically at Nikki as the woman tried to stop the blood from flowing out of her injured arm. Nikki glared at Matty as Phoenix agents swarmed around her, grabbing Nikki and pulling her upright. She was hauled away to one of the awaiting vehicles in a stony silence, not saying anything to anyone. Matty made sure she was secure in the vehicle before she walked over to her other agents.

Jack hurried over to his friend and extended his hand, which Mac gratefully accepted. The blond was hauled up, and Jack looked him over.

"You okay?" Jack asked as Mac dusted himself off.

"Yeah," Mac assured his partner. "The bullet didn't hit me. Aside from a few bumps and bruises, I'm fine. What about-"

"Sarah already had her people get Berkhoff outta here and taken to the nearest CIA facility to be treated. Once we're cleared to get outta here, we can go get him and take him home," Jack explained. MacGyver looked at Sarah, who was standing right behind Jack.

"Thanks," he said.

"Of course," Sarah replied with a small smile. "I'm definitely not one to pass up on the opportunity to save Jack's butt," she added. Jack mimicked her talking playfully, and Sarah chuckled before her face fell slightly, and she turned and began walking away. Jack looked after the woman as she walked, unsure of what to do. Jack glanced over at his partner, who raised his eyebrows.

"I think there's something you need to say to her," Mac said quietly. Jack looked back at the brunette walking away, hesitating for another minute until a gentle shove from Mac sent him stumbling after the woman.

"Hey, Sarah!" Jack called out. Mac watched as Sarah paused, and the two older agents began talking. He turned back to Matty to give his friend some privacy.

"Thanks," he said. "Things probably would have been a lot different if you hadn't shown up when you did," he added.

"We ran into with Sarah and her agents near the bottom of the mountain and decided that it would be best if we split up and covered the house from both angles. Looks like that was a good idea," she said.

"Yeah," Mac replied with a chuckle as he watched the last few guards being rounded up by both Phoenix and CIA agents. "That's definitely not an exaggeration." The two of them stood there for a moment, watching the proceedings around them, and then Mac spoke again. "What's going to happen now?" he asked. Matty gave him a questioning look, and he expounded a little further. "Are you gonna stay on as director, or are you going back to Homeland Security?" he asked. He was conflicted about what he wanted his answer to be. He respected Matilda Webber to no end, and she was a good leader, but now that Thornton was back in the picture, he didn't know what he really wanted. Matty observed the blond agent for a moment before answering.

"There are a few options that are being looked at," she said, purposefully not telling him any of the options that had been discussed in the short amount of time that she and Oversight had been able to talk about it. "We haven't made a final decision yet," she promised him. "And I'm sure we'll discuss it with you guys before anything final _is_ decided," she added. Mac nodded in appreciation, and Matty went to make sure Nikki didn't go anywhere, while Mac turned to wait for his partner.

 _0-0-0_

"Hey Sarah," Jack called out as he hurried towards the woman. Sarah stopped walking and turned around, a wary look in her eyes as she tried to figure out what Jack was coming to say. She prepared herself to tell him that she was very happily married still, and that he had missed his chance, but the words that came out of his mouth shocked her.

"I'm sorry," he said. Her mouth opened and closed as she floundered for words that weren't coming.

"Wait, what?" she asked, not sure if she'd heard him correctly.

"I'm sorry," Jack repeated. "Please don't make me say it again," he added with a mock pained expression.

"You're sorry for what?" Sarah asked, though she had a feeling she already knew what he was talking about.

"Y'know...back before your wedding. I was kind of a jerk," Jack explained. Sarah raised her eyebrow.

"Kind of?"

"Okay, I was more than 'kind of' a jerk," Jack conceded. "I had my shot with you and I didn't take it. It wasn't fair of me to try and convince you not to marry Jared-I mean Jeff," he corrected when he saw Sarah's expression. "Anyway, what I'm trying to tell you is that I hope you're happy, and I'm sorry for being such massive jerk," he finished. Sarah looked at him with a look of respect, admiration, and gratitude.

"Thank you, Jack," she said. "That means a lot."

Jack nodded his head, turning around quickly before he was able to make a fool of himself again, but he faced her one last time to say something else. "Also, thank you," he added. "For coming to get us," he said. "I don't things would have turned out as well as they did if you hadn't shown up," he said. His eyes went wide as he realized what he said. "Don't tell Matty I said that," he begged.

"Your secret's safe with me," Sarah promised with a wink. He gave her a grateful look, and Sarah stared at Jack softly. She finally leaned forward and gave him a kiss on the cheek before whispering in his ear, "I hope you find someone who loves you as much as I did."

Jack's mind immediately flashed to Diane, Riley's mother, but his attention refocused on Sarah as she placed her hands on his shoulders. "You haven't seen the last of me, Dalton," she said in a lighter tone. "You can expect me to be dropping by and checking up on Nikki," she said.

"See ya 'round, then," Jack said with a small smile. As Sarah turned and walked away, Jack expected to feel a pang of regret, but instead he felt a sense of relief wash over him. He had held onto his feelings for her for so long, but he knew now that he had let her go, and they were both able to move on. Things with he and Diane were progressing, slowly but surely, and now that he had closure with Sarah, he knew he could move on with Diane.

Jack turned and walked in the opposite direction, towards his partner who was still waiting for him, and together the two of them made their way to the Phoenix vehicles. Nikki had been restrained very securely, and Mac made sure they went through and removed all bobby pins from her person, and he also had them handcuff her hands behind her back so that she couldn't escape as easily as she had the first time. They also had agents sit on both sides of her in the backseat to keep an eye on her. Once they made sure she was secure, MacGyver and Jack climbed into another vehicle and the Phoenix convoy took off, heading back to Phoenix HQ.

 _ **So...thoughts? Too corny? Too cheesy? Too short? Too long? Lol let me know what you thought!**_


	12. Chapter 12

_**Guys I'm so sad this is the last chapter! *cries hardcore* I've literally had this open on my computer tab since like, February working on it, so it feels really weird to be closing the tab...**_

 _ **Longer AN at the bottom :)**_

 _ **Characters are not mine**_

MacGyver walked down the hallway towards Thornton's recovery room, stopping in the hallway as he saw two people standing in the room with Thornton. His adrenaline began pumping for a moment as he thought it was someone else from The Organization, but he calmed down when he realized it was just a member of Oversight (whose name Mac was pretty sure was Elana) and one of the doctors charged with looking after Thornton. Everyone looked up at MacGyver as he walked in, pausing their conversation for a moment before the doctor finished speaking

"Your stitches are healing up nicely," he commented as he looked over Thornton's charts. "We'll need to run a few more tests to make sure your blood is being filtered through your kidney alright, but I'm not expecting there to be any difficulties. Once we make sure everything is in working condition, I would say you should stay here for another day or so, but then I think you should be good to go home," the doctor explained with a smile as he looked up at the brunette.

"Thank you, Dr. Marsh," the woman from Oversight said. Dr. Marsh nodded and walked out, gently squeezing past MacGyver as he left the room. "Mr. MacGyver," Elana said as she looked at the young agent who was watching the doctor walk away.

"Yes ma'am?" Mac said, pulling his gaze back into the room.

"I hear we have you to thank for this?" she replied, gesturing to Thornton. "You helped rescue Patricia from members of The Organization, and you helped bring Agent Berkhoff home," she explained. Berkhoff had been retrieved from the CIA medical center and brought back to the Foundation, and he was in another recovery room just a few doors down.

"Thank you ma'am, but it was a team effort," Mac said. "I couldn't have done it without any of them, and that includes Thornton," he added, nodding at the woman lying on the bed. "She and Matty both had huge parts in helping everyone get home safely."

"Yes, I'm aware of that," Elana assured Mac with a calm tone. She turned to Thornton next. "Patricia, I'm ordering that you take as much time as you need to heal and recover, but after that, we would love to have you back with the Phoenix if you're willing," she said. Thornton looked like she was about to reply, but there was some noise coming from the outside the room, and the three occupants of the room turned to look in the hallway.

Nikki was being led through the halls, having just come from her own examination room for the wound in her arm, and she stared at the ground, no expression on her face at all.

"Wait," Thornton requested as she saw Nikki being led past. She slowly got to her feet, against Mac's and Elana's urgings to stay in bed, and made her way over to the traitor. Nikki stared at Thornton with cold eyes as her former boss finally stood face-to-face with the woman who had framed her, who had taken away so much.

There were no words exchanged between the two of them; just cold, icy stares. Nikki broke off the staring contest after a few moments and looked at Mac, who tried to keep his face as impassive as he could.

"Get her out of here," Elana finally ordered. Nikki was moved forward firmly, but she kept her head turned towards Mac for as long as she could, until they rounded the corner. No words had been spoken, but Mac felt like their encounter had contained a million words.

They watched the company disappear, and after a few more moments, Thornton made her way back towards her bed. Elana turned to watch the woman, waiting until Thornton leaned back on the bed before asking, "Have you and Matilda talked about what you want to do?"

Thornton nodded. Mac looked a little confused, but he remembered what Matty had told him about the choices she and Thornton were needing to make. "We decided for the time being to try co-directing, at least while I'm still down, and if we find that we just can't co-direct, one of us will become a field agent."

Elana nodded. "I respect that decision. It would have been a hard choice for us at Oversight to make, so we're glad things were able to be worked out peacefully." With that, the woman turned and walked out of the room, trailing after Nikki's escort, intent on making sure the traitor didn't escape.

There was a slightly awkward silence as Mac stood there, but he finally began talking. "I'm glad you're coming back," he admitted.

"Me too," Thornton replied, slightly surprising Mac; it wasn't a bad surprise though. He'd wondered if Thornton had hard feelings towards the Foundation after she had been arrested, but it appeared that she didn't.

"So you think it'll work with co-directing with Matty?" he asked.

"I'm going into it with an open mind," Thornton replied. "It's going to be new for both of us, and we're going to need to work things out. But yes, I'm hoping it will work," she added. Mac was about to reply, but his phone vibrated and he glanced down, seeing it was a text from his partner.

"You don't have to babysit me," Thornton reminded Mac with a smirk. "Go watch the game with Jack."

"How did-"

"I knew that Jack's favorite team was playing on the day I was broken out, and I'm assuming that you guys were called in immediately. With everything that's gone on since then, you haven't had time to watch it yet. Jack never misses their games if he can help it, and now that things have calmed down…"

Mac chuckled. "I forgot how good you were," he admitted. Thornton smirked at him again, but she could see the blond was still hesitant to leave her alone.

"Mac, it's been a long few days, and I'm honestly just planning on getting some rest," she informed him. "Go," she ordered gently. Mac finally nodded. He wasn't necessarily thrilled about watching the game (he'd googled the outcome and knew who won, and he knew Jack wouldn't be happy), but seeing the exhaustion in Thornton's eyes convinced him that she needed to sleep.

"'Kay," he finally relented. "I'll be back later," he promised. His phone vibrated again, and he read the text, a small chuckle escaping him. "Jack wants me to tell you he's glad you're not dead but that if I'm not there in twenty minutes he's gonna come over here and grab me himself," Mac added.

"Sounds like Jack," Thornton said with a small smile. "Just go, get out of here. If Jack comes over here, he'll just talk and talk, and there'll be no way that I'll get any rest," she said drily.

"Yes ma'am," Mac said with a grin, turning and walking out of Thornton's room to go home. After the blond walked out, Thornton laid back in her bed, closing her eyes and simply leaning back into the bed. She was relieved; now that her name was on the road to being cleared, she was going to be staying at the Phoenix medical center simply as a patient, and not as a prisoner.

 _0-0-0_

"No, no, no, no!" Jack yelled at the TV. Like Mac knew, the game was not going the way Jack wanted. "C'mon, man!" Jack griped as he watched his players shuffle off the field in defeat. Mac smirked to himself. He debated whether he should say it or not, and finally the temptation was just too great.

He leaned over and nudged Jack with his elbow. "You know," he said once his partner was looking at him. "That's an instance where those extra five seconds could have come in handy," he pointed out. Jack looked confused for a minute, then he remembered what had happened with the champagne bottle in Nikki's basement, and he glared at his partner.

"You wantin' to start somethin', boy?" he growled jokingly.

"Only if it'll take less than five seconds," Mac retorted. Jack glared again, and quick as lightning Jack had grabbed the young man and trapped him in a headlock. Bozer yelped slightly as the pair jerked next to him on the couch, and Mac's roommate leapt up as Mac's legs flailed wildly around while he fought against the headlock Jack had him in.

After a few moments, Jack let go of his friend, and Mac sat back panting, brushing his hair back into place. He made a face at Jack and scooted a little ways away, keeping out of his partner's reach.

"Y'all're crazy," Bozer informed them from where he was standing. "I'm gonna leave you two to work out your differences and go make some celebratory wings," he added proudly, cackling as he turned and walked into the kitchen.

"Smug little…" Jack began, letting the rest of his phrase trail off as he covered his face with his hands and let out a groan. "They lost," he complained. "To _Bozer's_ team?!"

"Sometimes that's just how it goes, man," Mac said, shrugging his shoulders in slight sarcasm in response to his friend's distress. Jack peered at his friend through his fingers, eyes narrowing as he detected his friend's sass. The two of them listened to Bozer humming some random tune in the kitchen, but after a few moments of that, Jack turned to his young friend.

"How're you doing?" he asked. Mac raised an eyebrow at him.

"With...?"

"C'mon man," Jack said. "You don't have to hide anything from me," he said. Mac sighed; he knew exactly what Jack was talking about. He'd just been hoping to avoid this conversation for a little bit longer. He opened his mouth to reply, but Jack cut him off before he could reply. "And don't even think about saying that you're fine," he cautioned, bringing his hands the rest of the way down from his face and pointing at Mac.

"I wasn't," Mac promised. "I was going to say that it sucks," he said. "I can't say that I didn't kind of see it coming though," he added. "Things had just felt a little off ever since she came back. I think I just didn't realize it sooner because...I _wanted_ her to be good. I should have known-"

"Dude, stop," Jack said, holding up his hand and stopping the blond's berating of himself. Mac paused mid-sentence, looking at Jack. "All of us should have known something was up," Jack said. "We should have looked harder into the evidence we found on Chrysalis. I'm not gonna tell you that things are gonna be okay, because I'm gonna tell you man," Jack said. "This next little while is probably...no, it's definitely gonna suck. But you don't have to do this alone," he added. "And hey, man, I know that sounds corny, but it's true. We were all duped by Nikki. The sting isn't as bad for us as it is for you, but we do have a small inkling of what you're going through," Jack said. "Just promise me that you're not going to keep all your feelings inside to try and deal with it yourself?" he asked. Mac looked at his friend, a huge wave of gratitude welling up inside him.

"Okay," he finally said. "I promise."

"Good," Jack said, sitting forward on the couch a little. "We're here for you, all of us," he said.

"I know," Mac replied. "And I don't think you'll ever know how much I appreciate it."

"Right back atcha, bro," Jack said. The older agent took a drink from his glass on the table, then looked at Mac. "I'm smelling those wings," he said. "Whaddya say we go see if Bozer's willing to share them with us?"

"Even if they're in celebration of your team's loss?" Mac asked in slight surprise.

"Chicken wings, man. Chicken wings," Jack said as he stood up. MacGyver let out a huff of laughter and shook his head slightly as Jack meandered towards the kitchen.

 _Yeah, Nikki betrayed us. Again. And it sucks. But like I said, if I'm being honest, I think I knew something was wrong, and her betrayal really comes as no surprise. I'm relieved Thornton isn't a traitor though. And like Jack said: I've got people around to support me if I need it, and I've got a feeling I'll be needing it._

"Mac, you comin'?" Jack called from the kitchen over Bozer's insistence that Jack get his filthy, loser-team hands off his celebratory wings. Mac grinned as he listened to his friend's banter.

 _The family hasn't felt complete without Thornton. Sure, Nikki had been a part of the team too, but while she was on the team, it didn't feel like a family. Now that Thornton's back, the family is starting to feel more like itself again. And I couldn't have asked for a better way to end the day._

 ** _WHEEEE CORNY, VERY-DELIWIEL CHEESY ENDING!_**

 ** _So? Whatcha think?_**

 ** _Thank you so much for all your support you guys. You honestly mean so much to me! Your kind words, follows, favorites, everything._**

 ** _I've got a few other stories in the works, one is pretty Riley-centric, which will probably be the next one I get out, unless I get an amazing idea for a one-shot...anyway. I'm always open to prompts, and if you've given me a prompt and you haven't seen it yet, let me know what it is again please! I promise I haven't forgotten about you, but with the whole moving situation, it's a little hard to remember everything!_**

 ** _I'll see you next time!_**


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